<PAGE>   1

                                                                    EXHIBIT 4(a)







                          THIRD SUPPLEMENTAL INDENTURE

                            Dated as of June 15, 2001

                                     between

                               SEMCO ENERGY, INC.,

                                    AS ISSUER

                                       and

                  BANK ONE TRUST COMPANY, NATIONAL ASSOCIATION,

                                   AS TRUSTEE










<PAGE>   2


                                TABLE OF CONTENTS

<TABLE>
<S>                                                                                                        <C>
ARTICLE I DEFINITIONS.......................................................................................1

         Section 1.1         Definition of Terms............................................................1

ARTICLE II ISSUE, EXECUTION, FORM AND REGISTRATION OF
SECURITIES..................................................................................................2

         Section 2.1         Authentication and Delivery of Securities......................................2
         Section 2.2         Execution of Securities........................................................2
         Section 2.3         Certificate of Authentication..................................................2
         Section 2.4         Form, Denomination and Date of Securities......................................2
         Section 2.5         Global Securities..............................................................5

ARTICLE III TERMS OF THE SECURITIES.........................................................................6

         Section 3.1         Terms of the Securities........................................................6
         Section 3.2         Form of the Securities........................................................10

ARTICLE IV MISCELLANEOUS...................................................................................10

         Section 4.1         Ratification of Indenture.....................................................10
         Section 4.2         Trustee Not Responsible for Recitals..........................................10
         Section 4.3         Governing Law.................................................................10
         Section 4.4         Separability..................................................................10
         Section 4.5         Counterparts..................................................................10
</TABLE>



<PAGE>   3


         THIRD SUPPLEMENTAL INDENTURE, dated as of June 15, 2001 (the "Third
Supplemental Indenture"), between SEMCO Energy, Inc., a corporation duly
organized and existing under the laws of the State of Michigan, (the "Company"),
and Bank One Trust Company, National Association, a national banking
association, as trustee (the "Trustee")

         WHEREAS, the Company executed and delivered the indenture, dated as of
October 23, 1998 (the "Base Indenture"), to the Trustee to provide for the
future issuance of the Company's debentures, notes, bonds or other evidences of
indebtedness (the "Securities"), to be issued from time to time in one or more
series as may be determined by the Company under the Base Indenture; and

         WHEREAS, the Company entered into a First Supplemental Indenture dated
as of June 16, 2000 and a Second Supplemental Indenture dated as of June 29,
2000 to the Base Indenture; and

         WHEREAS, pursuant to the terms of the Base Indenture, the Company
desires to provide for the establishment of a new series of its Securities to be
known as its 8% Senior Notes Due 2016 (the "8% Senior Notes Due 2016" or the
"Securities"), the form and substance of the Securities and the terms,
provisions and conditions thereof to be set forth as provided in the Base
Indenture as heretofore supplemented and as further supplemented by this Third
Supplemental Indenture (together, the "Indenture"); and

         WHEREAS, the Company has requested that the Trustee execute and deliver
this Third Supplemental Indenture and all requirements necessary to make this
Third Supplemental Indenture a valid instrument in accordance with its terms,
and to make the Securities, when executed by the Company and authenticated and
delivered by the Trustee, the valid obligations of the Company and all acts and
things necessary have been done and performed to make this Third Supplemental
Indenture enforceable in accordance with its terms, and the execution and
delivery of this Third Supplemental Indenture has been duly authorized in all
respects.

         NOW THEREFORE, in consideration of the purchase and acceptance of the
Securities by the Holders thereof, and for the purpose of setting forth, as
provided in the Indenture, the form and substance of the Securities and the
terms, provisions and conditions thereof, the Company covenants and agrees with
the Trustee as follows:


                                   ARTICLE I.
                                   DEFINITIONS

SECTION 1.1. Definition of Terms.

         Unless the context otherwise requires a term defined in the Indenture
has the same meaning when used in this Third Supplemental Indenture.


                                       1
<PAGE>   4

                                   ARTICLE II
              ISSUE, EXECUTION, FORM AND REGISTRATION OF SECURITIES

SECTION 2.1 AUTHENTICATION AND DELIVERY OF SECURITIES.

         Upon the execution and delivery of this Third Supplemental Indenture,
or from time to time thereafter, Securities in an aggregate principal amount not
in excess of $60,000,000 (or such higher amount as may be authorized by a
resolution of the Board of Directors of the Company or a committee thereof) may
be executed by the Company and delivered to the Trustee for authentication, and
the Trustee shall thereupon authenticate and deliver said Securities to or upon
the written order of the Company, signed by both (a) its Chairman of the Board
of Directors, or its President or any Vice President and (b) by its Chief
Financial Officer, or its Secretary or any Assistant Secretary, or its Treasurer
or any Assistant Treasurer without any further action by the Company. The
Securities shall be direct, unconditional obligations of the Company and shall
rank pari passu without preference among themselves and equally in priority of
payment with all other present and future, unsecured senior indebtedness of the
Company.

SECTION 2.2 EXECUTION OF SECURITIES.

         The Securities shall be signed on behalf of the Company by both (a) its
Chairman of the Board of Directors or its President or any Vice President and
(b) attested by its Secretary or its Assistant Secretary under its corporate
seal. Such signatures may be the manual or facsimile signatures of the present
or any future such officers. The seal of the Company may be in the form of a
facsimile thereof and may be impressed, affixed, imprinted or otherwise
reproduced on the Securities. Typographical and other minor errors or defects in
any such reproduction of the seal or any such signature shall not affect the
validity or enforceability of any Security that has been duly authenticated and
delivered by the Trustee.

SECTION 2.3 CERTIFICATE OF AUTHENTICATION.

         Only such Securities as shall bear thereon a certificate of
authentication substantially in the form recited in the form of Security
attached as Exhibit A hereto, executed by the Trustee by manual signature of one
of its authorized signatories, shall be entitled to the benefits of this
Indenture or be valid or obligatory for any purpose. Such certificate by the
Trustee upon any Security executed by the Company shall be conclusive evidence
that the Security so authenticated has been duly authenticated and delivered
hereunder and that the Holder is entitled to the benefits of this Indenture.

SECTION 2.4 FORM, DENOMINATION AND DATE OF SECURITIES.

         (a) The Securities and the Trustee's certificate of authentication
shall be substantially in the form set forth in the form of Security attached as
Exhibit A hereto. The Securities shall be numbered, lettered, or otherwise
distinguished in such manner or in accordance with such plans as the officers of
the Company executing the same may determine with the approval of the Trustee.



                                       2
<PAGE>   5

         Any of the Securities may be issued with appropriate insertions,
omissions, substitutions and variations and may have imprinted or otherwise
reproduced thereon such legend or legends, not inconsistent with the provisions
of this Indenture, as may be required to comply with any law or with any rules
or regulations pursuant thereto, or with the rules of any securities market in
which the Securities are admitted to trading, or to conform to general usage.

         (b) (i) This Section 2.4(b)(i) shall apply only to Securities in global
form ("Global Securities") deposited with The Depository Trust Company (the
"U.S. Depositary").

         The Company shall execute and the Trustee shall, in accordance with
this Section 2.4(b)(i), authenticate and deliver initially Global Securities
that (a) shall be registered in the name of the U.S. Depositary for such Global
Securities or the nominee of such U.S. Depositary, (b) shall be deposited on
behalf of Agent Members (as defined herein) with the Trustee as custodian for
the U.S. Depositary and (c) shall bear legends substantially to the following
effect:

         "UNLESS THIS CERTIFICATE IS PRESENTED BY AN AUTHORIZED REPRESENTATIVE
         OF [INSERT NAME AND ADDRESS OF U.S. DEPOSITARY] TO THE COMPANY OR ITS
         AGENT FOR REGISTRATION OF TRANSFER, EXCHANGE OR PAYMENT, AND ANY
         CERTIFICATE ISSUED IN EXCHANGE FOR THIS CERTIFICATE OR ANY PORTION
         HEREOF IS REGISTERED IN THE NAME OF [INSERT NAME OF U.S. NOMINEE OF
         DEPOSITARY], OR TO SUCH OTHER ENTITY AS IS REQUESTED BY AN AUTHORIZED
         REPRESENTATIVE OF [INSERT NAME OF U.S. DEPOSITARY], OR SUCH OTHER NAME
         AS IS REQUESTED BY AN AUTHORIZED REPRESENTATIVE OF [INSERT NAME OF U.S.
         DEPOSITARY] (AND ANY PAYMENT HEREON IS MADE TO [INSERT NAME OF NOMINEE
         OF U.S. DEPOSITARY]), ANY TRANSFER, PLEDGE OR OTHER USE HEREOF FOR
         VALUE OR OTHERWISE BY OR TO ANY PERSON OTHER THAN (INSERT NAME OF U.S.
         DEPOSITARY OR A NOMINEE THEREOF] IS WRONGFUL INASMUCH AS THE REGISTERED
         OWNER HEREOF, [INSERT NAME OF NOMINEE OF U.S. DEPOSITARY] HAS AN
         INTEREST HEREIN".

         "TRANSFERS OF THIS GLOBAL SECURITY SHALL BE LIMITED TO TRANSFERS IN
         WHOLE, BUT NOT IN PART, TO NOMINEES OF [INSERT NAME OF U.S. DEPOSITARY]
         OR TO A SUCCESSOR THEREOF OR SUCH SUCCESSOR'S NOMINEE AND TRANSFERS OF
         PORTIONS OF THIS GLOBAL SECURITY SHALL BE LIMITED TO TRANSFERS MADE IN
         ACCORDANCE WITH THE RESTRICTIONS SET FORTH IN SECTION 305 OF THE
         INDENTURE REFERRED TO ON THE REVERSE HEREOF".

         Members of, or participants in, a U.S. Depositary ("Agent Members")
shall have no rights under this Indenture with respect to any Global Security
held on their behalf by the U.S. Depositary or under any Global Security, and
the U.S. Depositary may be treated by the Company, the Trustee, and any agent of
the Company or the Trustee as the absolute owner of such Global Security for all
purposes whatsoever. Notwithstanding the foregoing, nothing herein shall prevent
the Company, the Trustee or any agent of the Company or the Trustee from giving




                                       3
<PAGE>   6

effect to any written certification, proxy or other authorization furnished by
the U.S. Depositary or impair, as between the U.S. Depositary and its Agent
Members, the operation of customary practices governing the exercise of the
rights of a holder of any security.

         (ii) This Section 2.4(b)(ii) shall apply only to the Global Security
deposited on behalf of the purchasers of the Securities represented thereby with
the Trustee as custodian for the U.S. Depositary for credit to their respective
accounts (or to such other accounts as they may direct) at Euroclear System
("Euroclear") or Cedel, S.A. ("Cedel") insofar as interests in the Global
Security are held by the Agent Members for Euroclear or Cedel.

         The provisions of the "Operating Procedures of the Euroclear System"
and the "Terms and Conditions Governing Use of Euroclear" and the "Management
Regulations" and "Instructions to Participants" of Cedel, respectively, shall be
applicable to such Global Security insofar as interests therein are held by the
Agent Members for Euroclear and Cedel. Account holders or participants in
Euroclear and Cedel shall have no rights under this Indenture with respect to
the Global Security, and the nominee of the U.S. Depositary may be treated by
the Company and the Trustee and any agent of the Company or the Trustee as the
owner of the Global Security for all purposes whatsoever. Notwithstanding the
foregoing, nothing herein shall prevent the Company, the Trustee or any agent of
the Company or the Trustee from giving effect to any written certification,
proxy or other authorization furnished by the U.S. Depositary or impair, as
between the U.S. Depositary and its Agent Members, the operation of customary
practices governing the exercise of the rights of a holder of any security.

         (c) Each Security shall be dated the date of its authentication and
shall bear interest from the applicable date, and shall be payable on the dates
specified on the face of the form of Security attached as Exhibit A hereto.

         (d) The Person in whose name any Security is registered at the close of
business on the record date specified in the Securities with respect to any
Interest Payment Date shall be entitled to receive the interest, if any, payable
on such Interest Payment Date notwithstanding any transfer or exchange of such
security subsequent to the record date and prior to such Interest Payment Date,
except if and to the extent the Company shall default in the payment of the
interest due on such Interest Payment Date, in which case such defaulted
interest shall be paid to the Persons in whose names Outstanding Securities are
registered at the close of business on a subsequent special record date, to be
established (together with the related payment date) by the Trustee. Such
special record date shall not be more than 15 nor less than 10 days prior to the
payment date. Not less than 10 days prior to the special record date, the
Company (or the Trustee, in the name of and the expense of the Company) shall
mail to Holders a notice that states the special record date, the related
payment date and the amount of interest to be paid. Notice of the proposed
payment of such defaulted interest and the special record date therefor having
been mailed as aforesaid, such defaulted interest shall be paid to the Persons
in whose names the Securities are registered on such special record date.

         (e) The Securities shall be issuable in the denominations specified in
the form of Security attached as Exhibit A hereto.



                                       4
<PAGE>   7

SECTION 2.5 GLOBAL SECURITIES.

         (a) Portions of a Global Security deposited with the U.S. Depositary
pursuant to Section 2.4 shall be transferred in certificated form to the
beneficial owners thereof only if such transfer complies with Section 305 of the
Base Indenture and (i) the U.S. Depositary notifies the Company that it is
unwilling or unable to continue as U.S. Depositary for such Global Security or
if at any time such U.S. Depositary ceases to be a "clearing agency" registered
under the Exchange Act and a successor depositary is not appointed by the
Company within 90 days of such notice, (ii) the Company determines not to have
the Securities represented by a Global Security, or (iii) an Event of Default
has occurred and is continuing with respect to the Securities and the beneficial
owners of a majority in interest of Securities have advised the U.S. Depositary
to cease acting as depository for the Securities.

         (b) Portions of any Global Security that are transferable to the
beneficial owners thereof pursuant to this Section 2.5 shall be surrendered by
the U.S. Depositary to the Trustee at its New York office for registration of
transfer, in whole or from time to time in part, without charge and the Trustee
shall authenticate and deliver, upon such registration of transfer of each
portion of such Global Security, an equal aggregate principal amount of
Securities of authorized denominations. Any portion of a Global Security whose
registration is transferred pursuant to this Section 2.5 shall be executed,
authenticated and delivered only in the denominations specified in the form of
Security attached as Exhibit A hereto and registered in such names as the U.S.
Depositary shall direct.

         (c) Subject to the provisions of Section 2.4(b) above, the registered
Holder of any Global Security may grant proxies and otherwise authorize any
person, including Agent Members and persons that may hold interests through
Agent Members, to take any action which a Holder is entitled to take under this
Indenture or the Securities.

         (d) In the event of the occurrence of any of the events specified in
paragraph (a) of this Section 2.5, the Company shall promptly make available to
the Trustee a reasonable supply of certificated Securities in definitive fully,
registered form without interest coupons.




                                       5
<PAGE>   8


                                   ARTICLE III

                                      TERMS

SECTION 3.1 TERMS OF THE SECURITIES.

The Securities contain the following terms and conditions:


TITLE OF SECURITIES:

         8% Senior Notes Due 2016

AGGREGATE PRINCIPAL AMOUNT:

         $60,000,000

MATURITY:

         June 30, 2016

INTEREST RATE:

         8% per annum

DATE FROM WHICH INTEREST ACCRUES:

         June 21, 2001, or from the most recent Interest Payment Date to which
interest has been paid or duly provided for.

INTEREST PAYMENT DATES:

         Quarterly on each March 31, June 30, September 30 and December 31
commencing September 30, 2001 and at maturity. In the event that any date on
which interest is payable is not a Business Day (as defined in the Indenture),
then payment of the interest payable on such date will be made on the next
succeeding day which is a Business Day.

REGULAR RECORD DATE:

         Payments of interest and principal shall be made to the person in whose
name a Series 8% Senior Note is registered at the close of business on the
fifteenth calendar day, whether or not a Business Day, prior to the payment
date.



                                       6
<PAGE>   9

PLACE OF PAYMENT

         Any designated office of the Trustee, including such office located in
the Borough of Manhattan.

REDEMPTION - COMPANY OPTION:

         Redeemable, in whole or in part, at any time on and after June 30, 2006
at a redemption price equal to 100% of the principal amount redeemed plus any
accrued and unpaid interest to the date of redemption.

REDEMPTION - LIMITED HOLDER OPTION

         For purposes of this provision, a "Beneficial Owner" means the person
who has the right to sell, transfer or otherwise dispose of an interest in a
Series 8% Senior Note and the right to receive the proceeds therefrom, as well
as the interest and principal payable to the holder thereof. In general, a
determination of beneficial ownership in the Series 8% Senior Notes will be
subject to the rules, regulations and procedures governing the depositary and
institutions that have accounts with the depositary or a nominee thereof
("Participants").

         Unless the Series 8% Senior Notes have been declared due and payable
prior to their maturity by reason of an event of default under the Indenture,
the Representative (defined below) of a deceased Beneficial Owner has the right
to request redemption of all or part of such Beneficial Owner's interest in the
Series 8% Senior Notes. The request must be expressed in multiples of $1,000.
The Company will redeem such Beneficial Owner's Series 8% Senior Notes subject
to the following limitations. The Company will not be obligated to redeem during
the period from the initial issuance of the Series 8% Senior Notes through and
including June 30, 2002 (the "Initial Period"), and during any twelve-month
period which ends on and includes each June 30 thereafter (each such
twelve-month period being hereinafter referred to as a "Subsequent Period") (i)
on behalf of any deceased Beneficial Owner, any interest in the Series 8% Senior
Notes which exceeds a principal amount of $60,000 and (ii) interests in the
Series 8% Senior Notes in an aggregate principal amount exceeding $1,200,000. A
request for redemption may be presented to the Trustee under the Indenture by
the Representative of a deceased Beneficial Owner at any time and in any
principal amount in integral multiples of $1,000, subject to the limitations set
forth above. Representatives of deceased Beneficial Owners must make
arrangements with the Participant in the depositary through whom such interest
is owned in order that timely presentation of redemption requests can be made by
the Participant and, in turn, by the depositary, to the Trustee. If the Company,
although not obligated to do so, chooses to redeem interests in the Series 8%
Senior Notes of a deceased Beneficial Owner during the Initial Period or in any
Subsequent Period in excess of the $60,000 limitation, such redemption, to the
extent that it exceeds the $60,000 limitation for any deceased Beneficial Owner,
shall not be included in the computation of the $1,200,000 aggregate limitation
for such Initial Period or such Subsequent Period, as the case may be.

         Subject to the $60,000 and the $1,200,000 limitations, the Company
will, upon the death of a Beneficial Owner, redeem the interest of such
Beneficial Owner in the Series 8% Senior



                                       7
<PAGE>   10

Notes within 60 days following receipt by the Trustee of a Redemption Request
(defined below), including all supporting documentation, from such Beneficial
Owner's representative, or surviving joint tenant(s), tenant(s) by the entirety
or tenant(s) in common, or other persons entitled to effect a Redemption Request
(each of which is a "Representative"). If, during the Initial Period or any
Subsequent Period, Redemption Requests exceed the aggregate principal amount of
Series 8% Senior Notes required to be redeemed, then such excess Redemption
Requests (subject in the case of the $60,000 limitation to the provisions of the
last sentence of the preceding paragraph) will be applied to successive
Subsequent Periods in order of receipt, regardless of the number of Subsequent
Periods required to redeem such interests unless sooner withdrawn as described
below.

         A request for redemption of an interest in the Series 8% Senior Notes
may be made by delivering a request to the Participant in the depositary through
whom the deceased Beneficial Owner owned such Series 8% Senior Notes, in form
satisfactory to the Participant, together with evidence of the death of the
Beneficial Owner and the authority of the Representative satisfactory to the
Participant and the Trustee. A Representative of a deceased Beneficial Owner may
make the request for redemption and shall submit such other evidence of the
right to such redemption as the Participant or the Trustee shall require. The
request shall specify the principal amount of Series 8% Senior Notes to be
redeemed. A request for redemption in form satisfactory to the Participant and
accompanied by the documents relevant to the request as above provided, together
with a certification by the Participant that it holds the interest on behalf of
the deceased Beneficial Owner with respect to whom the request for redemption is
being made (a "Redemption Request"), must be provided to the depositary by a
Participant, and the depositary will forward the request to the Trustee.
Redemption Requests, including all supporting documentation, must be in the form
satisfactory to the Trustee, and no request for redemption will be considered
validly made until the Redemption Request and all supporting documentation, in
form satisfactory to the Trustee, have been received by the Trustee.

         The price to be paid by the Company for an interest in the Series 8%
Senior Notes to be redeemed pursuant to the request of a Representative of a
deceased Beneficial Owner is 100% of the principal amount thereof plus accrued
and unpaid interest, if any, to the date of payment. Subject to arrangements
with the depositary, payment for interests in the Series 8% Senior Notes which
are to be redeemed will be made to the depositary within 60 days following
receipt by the Trustee of the Redemption Request, including all supporting
documentation, and the Series 8% Senior Notes in the aggregate principal amount
specified in the Redemption Requests submitted to the Trustee by the depositary
which are to be fulfilled in connection with such payment. Any acquisition of
Series 8% Senior Notes by the Company or its subsidiaries other than by
redemption at the option of a Representative of a deceased Beneficial Owner
shall not be included in the computation of either the $60,000 or the $1,200,000
limitation for the Initial Period or for any Subsequent Period.

         Interests in the Series 8% Senior Notes held in tenancy by the
entirety, joint tenancy or by tenants in common will be deemed to be held by a
single Beneficial Owner, and the death of a tenant in common, tenant by the
entirety or joint tenant will be deemed the death of a Beneficial Owner. The
death of a person who, during such person's lifetime, was entitled to
substantially all of the rights of a Beneficial Owner of the Series 8% Senior
Notes will be deemed the death of


                                       8
<PAGE>   11

the Beneficial Owner, regardless of the recordation of such interest on the
records of the Participant in the depositary, if such rights can be established
to the satisfaction of the participant and the Trustee. Such interest shall be
deemed to exist in typical cases of nominee ownership, ownership under the
Uniform Gifts to Minors Act or the Uniform Transfers to Minors Act, community
property or other similar joint ownership arrangements, including individual
retirement accounts or Keogh [H.R. 10] plans maintained solely by or for the
decedent or by or for the decedent and any spouse, and trust and certain other
arrangements where one person has substantially all of the rights of a holder
during such person's lifetime.

         In the case of a Redemption Request which is presented on behalf of a
deceased Beneficial Owner and which has not been fulfilled at the time the
Company gives notice of its election to redeem the Series 8% Senior Notes, the
Series 8% Senior Notes which are the subject of such Redemption Request shall
not be eligible for redemption pursuant to the Company's option to redeem but
shall remain subject to redemption pursuant to such Redemption Request. Subject
to the provisions of the immediately preceding sentence, any Redemption Request
may be withdrawn upon delivery of a written request for such withdrawal given to
the Trustee by the depositary prior to payment for redemption of interests in
the Series 8% Senior Notes by reason of the death of a Beneficial Owner.

         The Company is legally obligated to redeem Series 8% Senior Notes
properly presented for redemption pursuant to a Redemption Request in accordance
with and subject to the terms, conditions and limitations in the Indenture, as
summarized above. The Company's redemption obligation is not cumulative. Nothing
in the Indenture prohibits the Company from redeeming, in fulfillment of the
Redemption Requests made pursuant to the Indenture, Series 8% Senior Notes in
excess of the principal amount that the Company is obligated to redeem, nor does
anything in the Indenture prohibit the Company from purchasing any Series 8%
Senior Notes in the open market. However, the Company may not use any Series 8%
Senior Notes redeemed or purchased as described in the immediately preceding
sentence as a credit against the Company's redemption obligation.

         Because of the limitations of the Company's requirement to redeem, no
Beneficial Owner can have any assurance that his or her Series 8% Senior Notes
will be paid prior to maturity.

SINKING FUND PROVISIONS:

         None

FORM:

         One or more permanent global notes in definitive, fully registered,
book-entry form, without coupons.

DEPOSITARY:

         The Depository Trust Company.




                                       9
<PAGE>   12

DEFEASANCE:

         The provisions of Sections 1402 and 1403 of the Indenture shall be
applicable to the Series 8% Senior Notes.

SECTION 3.2 FORM OF THE SECURITIES.

         The form of the Series 8% Senior Notes shall be the form set forth in
Exhibit A attached hereto.

                                   ARTICLE IV
                                  MISCELLANEOUS

SECTION 4.1. Ratification of Indenture.

         The Indenture as supplemented by this Third Supplemental Indenture, is
in all respects ratified and confirmed, and this Third Supplemental Indenture
shall be deemed part of the Indenture in the manner and to the extent herein and
therein provided.

SECTION 4.2. Trustee Not Responsible for Recitals.

         The recitals herein contained are made by the Company and not by the
Trustee, and the Trustee assumes no responsibility for the correctness thereof.
The Trustee makes no representation as to the validity or sufficiency of this
Third Supplemental Indenture.

SECTION 4.3. Governing Law.

         This Third Supplemental Indenture and each Security shall be deemed to
be a contract made under the internal laws of the State of New York, and for all
purposes shall be construed in accordance with the laws of said State, without
regard to conflicts of laws principles.

SECTION 4.4. Separability.

         In case any one or more of the provisions contained in this Third
Supplemental Indenture or in the Securities shall for any reason be held to be
invalid, illegal or unenforceable in any respect, such invalidity, illegality or
unenforceability shall not affect any other provisions of this Third
Supplemental Indenture or of the Securities, but this Third Supplemental
Indenture and the Securities shall be construed as if such invalid or illegal or
unenforceable provision had never been contained herein or therein.

SECTION 4.5. Counterparts.

         This Third Supplemental Indenture may be executed in any number of
counterparts each of which shall be an original; but such counterparts shall
together constitute but one and the same instrument.



                                       10
<PAGE>   13

         IN WITNESS WHEREOF, the parties hereto have caused this Third
Supplemental Indenture to be duly executed by their respective officers
thereunto duly authorized, on the date or dates indicated in the acknowledgments
and as of the day and year first above written.

                               SEMCO ENERGY, INC.
                               as Issuer

                               By:
                                  ----------------------------------------------
                                  Name:    Marcus Jackson
                                  Title:   President and Chief Executive Officer

                               BANK ONE TRUST COMPANY, NATIONAL
                               ASSOCIATION, as Trustee

                               By:
                                  ----------------------------------------------
                                  Name:
                                  Title:





                                       11
<PAGE>   14



                                                                       Exhibit A

Unless this certificate is presented by an authorized representative of The
Depository Trust Company, a New York corporation ("DTC"), to the Corporation or
its agent for registration of transfer, exchange or payment, and any certificate
issued is registered in the name of Cede & Co. or in such other name as is
requested by an authorized representative of DTC (and any payment is made to
Cede & Co. or to such other entity as is requested by an authorized
representative of DTC), ANY TRANSFER, PLEDGE, OR OTHER USE HEREOF FOR VALUE OR
OTHERWISE BY OR TO ANY PERSON IS WRONGFUL inasmuch as the registered owner
hereof, Cede & Co., has an interest herein.



                                                           CUSIP NO. 78412D AE 9


No.                             SEMCO ENERGY, INC.
   --
                             SERIES 8% SENIOR NOTES
                                    DUE 2016


<TABLE>
<S>                                 <C>
Principal Amount:                   $60,000,000

Regular Record Date:                The fifteenth calendar day, whether or not a Business Day,
                                    prior to the Interest Payment Date

Original Issue Date:                June 21, 2001

Maturity:                           June 30, 2016

Interest Payment Dates:             Quarterly on each March 31, June 30, September 30 and
                                    December 31 commencing on September 30, 2001

Interest Rate:                      8% per annum

Authorized Denomination:            $1,000 or any integral multiples thereof

Place of Payment:                   Any designated office of the Trustee, including such office
                                    located in the Borough of Manhattan.
</TABLE>

         SEMCO Energy, Inc., a Michigan corporation (the "Corporation", which
term includes any successor corporation under the Indenture referred to on the
reverse hereto), for value received, hereby promises to pay to CEDE & CO. or its
registered assigns, the principal sum of SIXTY MILLION DOLLARS ($60,000,000) on
the Maturity shown above, unless redeemed prior thereto as hereinafter provided,
and to pay interest thereon from the Original Issue Date



                                        1
<PAGE>   15

shown above, or from the most recent Interest Payment Date to which interest has
been paid or duly provided for, in arrears on each Interest Payment Date as
specified above in each year, commencing on September 30, 2001, at the rate per
annum shown above (the "Interest Rate") until the principal hereof (and premium,
if any) is paid or made available for payment and on any overdue principal (and
premium, if any) and on any overdue installment of interest. The interest so
payable, and punctually paid or duly provided for, on any Interest Payment Date
will, as provided in such Indenture, be paid to the Person in whose name this
Series 8% Senior Note (this "Security") is registered at the close of business
on the Regular Record Date as specified above next preceding such Interest
Payment Date. Except as otherwise provided in the Indenture, any such interest
not so punctually paid or duly provided for will forthwith cease to be payable
to the Holder on such Regular Record Date and may either be paid to the Person
in whose name this Security is registered at the close of business on a Special
Record Date for the payment of such Defaulted Interest to be fixed by the
Trustee, notice whereof shall be mailed to Holders of Securities of this series
not less than 10 days prior to such Special Record Date, or be paid at any time
in any other lawful manner not inconsistent with the requirements of any
securities exchange, if any, on which the Securities of this series shall be
listed, and upon such notice as may be required by any such exchange, all as
more fully provided in said Indenture.

         Interest payments for this Security shall be computed and paid on the
basis of a 360-day year of twelve 30-day months. In the event that any date on
which principal (and premium, if any) or interest is payable on this Security is
not a Business Day, then payment of the principal (and premium, if any) or
interest payable on such date will be made on the next succeeding day that is a
Business Day (and without any interest or payment in respect of any such delay)
with the same force and effect as if made on the date the payment was originally
payable.

         Payment of the principal (and premium, if any) of this Security, when
due and payable, shall be made upon surrender of this Security, at any Place of
Payment, in such coin or currency of the United States of America as at the time
of payment is legal tender for payment of public and private debts. At the
option of the Corporation, all payments of principal may be made by check to the
registered holder of the Security or such other person entitled thereto against
surrender of such Security. Payment of interest will be made, at the option of
the Corporation, (i) by check mailed to the address of the Person entitled
thereto as such address shall appear in the Security Register or (ii) by wire
transfer to an account maintained by the Person entitled thereto located inside
the United States.

         REFERENCE IS HEREBY MADE TO THE FURTHER PROVISIONS OF THIS SECURITY SET
FORTH ON THE REVERSE HEREOF, WHICH FURTHER PROVISIONS SHALL FOR ALL PURPOSES
HAVE THE SAME EFFECT AS IF SET FORTH AT THIS PLACE.

         Unless the certificate of authentication hereon has been executed by
the Trustee by manual signature, this Security shall not be entitled to any
benefit under the Indenture or be valid or obligatory for any purpose.





                                        2
<PAGE>   16


         IN WITNESS WHEREOF, the Corporation has caused this instrument to be
duly executed under its corporate seal.

Dated:  June 21, 2001


                                       SEMCO ENERGY, INC.


                                       By:
                                          --------------------------------------
                                          Marcus Jackson
                                          President and Chief Executive Officer

Attest:

--------------------------------------
Sherry L. Abbott, Secretary



                          CERTIFICATE OF AUTHENTICATION

      This is one of the Securities of the series designated therein referred to
in the within-mentioned Indenture.

                                       BANK ONE TRUST COMPANY, NATIONAL
                                       ASSOCIATION, as Trustee


                                       By:
                                          --------------------------------------



                                       3

<PAGE>   17




                           (Reverse Side of Security)


         This Security is one of a duly authorized issue of Securities of the
Corporation (the "Securities"), issued and issuable in one or more series under
an Indenture, dated as of October 23, 1998 as supplemented by a First, Second
and Third Supplemental Indenture (the "Indenture"), between the Corporation and
Bank One Trust Company, National Association, successor to NBD Bank, as Trustee
(the "Trustee", which term includes any successor trustee under the Indenture),
to which Indenture reference is hereby made for a statement of the respective
rights, limitation of rights, duties and immunities thereunder of the
Corporation, the Trustee and the Holders of the Securities issued thereunder and
of the terms upon which said Securities are, and are to be, authenticated and
delivered. This Security is one of the series designated on the face hereof as
Series 8% Senior Notes Due 2016 (the "Series 8% Senior Notes" or "Securities of
this series") in the aggregate principal amount of up to $60,000,000.
Capitalized terms used herein for which no definition is provided herein shall
have the meanings set forth in the Indenture.

         The Securities of this series are redeemable, in whole or in part, at
any time on or after June 30, 2006 at a redemption price equal to 100% of the
principal amount redeemed plus any accrued and unpaid interest to the date of
redemption.

         For purposes of this provision, a "Beneficial Owner" means the person
who has the right to sell, transfer or otherwise dispose of an interest in a
Series 8% Senior Note and the right to receive the proceeds therefrom, as well
as the interest and principal payable to the holder thereof. In general, a
determination of beneficial ownership in the Series 8% Senior Notes will be
subject to the rules, regulations and procedures governing the depositary and
institutions that have accounts with the depositary or a nominee thereof
("Participants").

         Unless the Series 8% Senior Notes have been declared due and payable
prior to their maturity by reason of an event of default under the Indenture,
the Representative (defined below) of a deceased Beneficial Owner has the right
to request redemption of all or part of such Beneficial Owner's interest in the
Series 8% Senior Notes. The request must be expressed in multiples of $1,000.
The Corporation will redeem such Beneficial Owner's Series 8% Senior Notes
subject to the following limitations. The Corporation will not be obligated to
redeem during the period from the initial issuance of the Series 8% Senior Notes
through and including June 30, 2002 (the "Initial Period"), and during any
twelve-month period which ends on and includes each June 30 thereafter (each
such twelve-month period being hereinafter referred to as a "Subsequent Period")
(i) on behalf of any deceased Beneficial Owner, any interest in the Series 8%
Senior Notes which exceeds a principal amount of $60,000 and (ii) interests in
the Series 8% Senior Notes in an aggregate principal amount exceeding
$1,200,000. A request for redemption may be presented to the Trustee under the
Indenture by the Representative of a deceased Beneficial Owner at any time and
in any principal amount in integral multiples of $1,000, subject to the
limitations set forth above. Representatives of deceased Beneficial Owners must
make arrangements with the Participant in the depositary through whom such
interest is owned in order that timely presentation of redemption requests can
be made by the Participant and, in turn, by the depositary, to the Trustee. If
the Corporation, although not obligated to do so, chooses to



                                       1
<PAGE>   18

redeem interests in the Series 8% Senior Notes of a deceased Beneficial Owner
during the Initial Period or in any Subsequent Period in excess of the $60,000
limitation, such redemption, to the extent that it exceeds the $60,000
limitation for any deceased Beneficial Owner, shall not be included in the
computation of the $1,200,000 aggregate limitation for such Initial Period or
such Subsequent Period, as the case may be.

         Subject to the $60,000 and the $1,200,000 limitations, the Corporation
will, upon the death of a Beneficial Owner, redeem the interest of such
Beneficial Owner in the Series 8% Senior Notes within 60 days following receipt
by the Trustee of a Redemption Request (defined below), including all supporting
documentation, from such Beneficial Owner's representative, or surviving joint
tenant(s), tenant(s) by the entirety or tenant(s) in common, or other persons
entitled to effect a Redemption Request (each of which is a "Representative").
If, during the Initial Period or any Subsequent Period, Redemption Requests
exceed the aggregate principal amount of Series 8% Senior Notes required to be
redeemed, then such excess Redemption Requests (subject in the case of the
$60,000 limitation to the provisions of the last sentence of the preceding
paragraph) will be applied to successive Subsequent Periods in order of receipt,
regardless of the number of Subsequent Periods required to redeem such interests
unless sooner withdrawn as described below.

         A request for redemption of an interest in the Series 8% Senior Notes
may be made by delivering a request to the Participant in the depositary through
whom the deceased Beneficial Owner owned such Series 8% Senior Notes, in form
satisfactory to the Participant, together with evidence of the death of the
Beneficial Owner and the authority of the Representative satisfactory to the
Participant and the Trustee. A Representative of a deceased Beneficial Owner may
make the request for redemption and shall submit such other evidence of the
right to such redemption as the Participant or the Trustee shall require. The
request shall specify the principal amount of Series 8% Senior Notes to be
redeemed. A request for redemption in form satisfactory to the Participant and
accompanied by the documents relevant to the request as above provided, together
with a certification by the Participant that it holds the interest on behalf of
the deceased Beneficial Owner with respect to whom the request for redemption is
being made (a "Redemption Request"), must be provided to the depositary by a
Participant, and the depositary will forward the request to the Trustee.
Redemption Requests, including all supporting documentation, must be in the form
satisfactory to the Trustee, and no request for redemption will be considered
validly made until the Redemption Request and all supporting documentation, in
form satisfactory to the Trustee, have been received by the Trustee.

         The price to be paid by the Corporation for an interest in the Series
8% Senior Notes to be redeemed pursuant to the request of a Representative of a
deceased Beneficial Owner is 100% of the principal amount thereof plus accrued
and unpaid interest, if any, to the date of redemption. Subject to arrangements
with the depositary, payment for interests in the Series 8% Senior Notes which
are to be redeemed will be made to the depositary within 60 days following
receipt by the Trustee of the Redemption Request, including all supporting
documentation, and the Series 8% Senior Notes in the aggregate principal amount
specified in the Redemption Requests submitted to the Trustee by the depositary
which are to be fulfilled in connection with such payment. Any acquisition of
Series 8% Senior Notes by the Corporation or its subsidiaries other than by
redemption at the option of a Representative of a deceased Beneficial Owner
shall




                                       2
<PAGE>   19

not be included in the computation of either the $60,000 or the $1,200,000
limitation for the Initial Period or for any Subsequent Period.

         Interests in the Series 8% Senior Notes held in tenancy by the
entirety, joint tenancy or by tenants in common will be deemed to be held by a
single Beneficial Owner, and the death of a tenant in common, tenant by the
entirety or joint tenant will be deemed the death of a Beneficial Owner. The
death of a person who, during such person's lifetime, was entitled to
substantially all of the rights of a Beneficial Owner of the Series 8% Senior
Notes will be deemed the death of the Beneficial Owner, regardless of the
recordation of such interest on the records of the Participant in the
depositary, if such rights can be established to the satisfaction of the
Participant and the Trustee. Such interest shall be deemed to exist in typical
cases of nominee ownership, ownership under the Uniform Gifts to Minors Act or
the Uniform Transfers to Minors Act, community property or other similar joint
ownership arrangements, including individual retirement accounts or Keogh [H.R.
10] plans maintained solely by or for the decedent or by or for the decedent and
any spouse, and trust and certain other arrangements where one person has
substantially all of the rights of a holder during such person's lifetime.

         In the case of a Redemption Request which is presented on behalf of a
deceased Beneficial Owner and which has not been fulfilled at the time the
Corporation gives notice of its election to redeem the Series 8% Senior Notes,
the Series 8% Senior Notes which are the subject of such Redemption Request
shall not be eligible for redemption pursuant to the Corporation's option to
redeem but shall remain subject to redemption pursuant to such Redemption
Request. Subject to the provisions of the immediately preceding sentence, any
Redemption Request may be withdrawn upon delivery of a written request for such
withdrawal given to the Trustee by the depositary prior to payment for
redemption of interests in the Series 8% Senior Notes by reason of the death of
a Beneficial Owner.

           The Corporation is legally obligated to redeem Series 8% Senior Notes
properly presented for redemption pursuant to a Redemption Request in accordance
with and subject to the terms, conditions and limitations in the Indenture, as
summarized above. The Corporation's redemption obligation is not cumulative.
Nothing in the Indenture prohibits the Corporation from redeeming, in
fulfillment of the Redemption Requests made pursuant to the Indenture, Series 8%
Senior Notes in excess of the principal amount that the Corporation is obligated
to redeem, nor does anything in the Indenture prohibit the Corporation from
purchasing any Series 8% Senior Notes in the open market. However, the
Corporation may not use any Series 8% Senior Notes redeemed or purchased as
described in the immediately preceding sentence as a credit against the
Corporation's redemption obligation.

         Because of the limitations of the Corporation's requirement to redeem,
no Beneficial Owner can have any assurance that his or her Series 8% Senior
Notes will be paid prior to maturity.

         If an Event of Default with respect to the Securities of this series
shall occur and be continuing, the principal of the Securities of this series
may be declared due and payable in the manner, with the effect and subject to
the conditions provided in the Indenture.




                                       3
<PAGE>   20

         The Indenture permits, with certain exceptions as therein provided, the
amendment thereof and the modification of the rights of the Holders of the
Securities of all series affected under the Indenture at any time by the
Corporation and the Trustee with the consent of the Holders of not less than a
majority in principal amount of the Outstanding Securities of all series
affected thereby (voting as one class). The Indenture contains provisions
permitting the Holders of not less than a majority in principal amount of the
Outstanding Securities of any series with respect to which a default under the
Indenture shall have occurred and be continuing (voting as one class), on behalf
of the Holders of the Securities of such series, to waive, with certain
exceptions, such default under the Indenture and its consequences. The Indenture
also permits the Holders of not less than a majority in principal amount of the
Securities of each series at the time Outstanding, on behalf of the Holders of
all Securities of such series, to waive compliance by the Corporation with
certain provisions of the Indenture affecting such series. Any such consent or
waiver by the Holder of this Security shall be conclusive and binding upon such
Holder and upon all future Holders of this Security and of any Security issued
upon the registration of transfer hereof or in exchange hereof or in lieu
hereof, whether or not notation of such consent or waiver is made upon this
Security.

         As provided in the Indenture and subject to certain limitations therein
set forth, the transfer of this Security is registrable in the Security
Register, upon surrender of this Security for registration of transfer at the
office or agency of the Corporation for such purpose, duly endorsed by, or
accompanied by a written instrument of transfer in form satisfactory to the
Corporation and the Security Registrar and duly executed by, the Holder hereof
or his attorney duly authorized in writing, and thereupon one or more new
Securities of this series, of authorized denominations and of like tenor and for
the same aggregate principal amount, will be issued to the designated transferee
or transferees. No service charge shall be made for any such registration of
transfer or exchange, but the Corporation may require payment of a sum
sufficient to cover any tax or other governmental charge payable in connection
therewith.

         As provided in and subject to the provisions of the Indenture, the
Holder of this Security shall not have the right to institute any proceeding
with respect to the Indenture or for the appointment of a receiver or trustee or
for any other remedy thereunder, unless such Holder shall have previously given
the Trustee written notice of a continuing Event of Default with respect to the
Securities of this series, the Holders of not less than 25% in principal amount
of the Securities of this series at the time Outstanding shall have made written
request to the Trustee to institute proceedings in respect of such Event of
Default as Trustee and offered the Trustee reasonable indemnity, and the Trustee
shall have failed to institute any such proceeding for 60 days after receipt of
such notice, request and offer of indemnity and shall not have received during
such 60-day period from the Holders of a majority in principal amount of
Securities of this series at the time Outstanding a direction inconsistent with
such request. The foregoing shall not apply to any suit instituted by the Holder
of this Security for the enforcement of any payment of principal hereof or any
interest hereon on or after the respective due dates expressed herein.

         The Indenture contains provisions for defeasance at any time of all or
a portion of the indebtedness of the Securities of this series and for covenant
defeasance at any time of certain covenants in the Indenture upon compliance
with certain conditions set forth in the Indenture.



                                       4
<PAGE>   21

         The Securities of this series are issuable only in registered form
without coupons in denominations of $1,000 and any integral multiple thereof. As
provided in the Indenture and subject to the limitations therein set forth,
Securities of this series are exchangeable for a like aggregate principal amount
of Securities of this series of any authorized denomination, as requested by the
Holder surrendering the same upon surrender of the Security or Securities to be
exchanged at any Place of Payment.

         Prior to the due presentment of a Security of this series for
registration of transfer, the Corporation, the Trustee and any agent of the
Corporation or Trustee may treat the registered Holder thereof as the owner of
such Security for the purpose of receiving payment of principal of (and premium,
if any) and (subject to certain Indenture provisions) interest on, such Security
and for all other purposes whatsoever, whether or not such Security be overdue,
and neither the Corporation, the Trustee nor any agent of the Corporation or the
Trustee shall be affected by notice to the contrary.

         This Security shall be governed by, and construed in accordance with,
the internal laws of the State of New York.



                                       5
<PAGE>   22


                                  ABBREVIATIONS

The following abbreviations, when used in the inscription on the face of this
instrument, shall be construed as though they were written out in full according
to applicable laws or regulations:

TEN COM - as tenants in common

TEN ENT - as tenants by the entireties

JT TEN - as joint tenants with rights
         of survivorship and not as
         tenants in common

UNIF GIFT MIN ACT - ..................... Custodian ............................
                          (Cust)                               (Minor)

Under Uniform Gifts to Minors Act...............................................
                                                  (State)

  Additional abbreviations may also be used though not on the above list.

--------------------------------------------------------------------------------

         FOR VALUE RECEIVED, the undersigned hereby sell(s) and transfers) unto
                (please insert Social Security or other identifying number of
assignee).


--------------------------------------------------------------------------------
PLEASE PRINT OR TYPEWRITE NAME AND ADDRESS, INCLUDING POSTAL ZIP CODE OF
ASSIGNEE

--------------------------------------------------------------------------------


--------------------------------------------------------------------------------
the within Security and all rights thereunder, hereby irrevocably constituting
and appointing agent to transfer said Security on the books of the Corporation,
with full power of substitution in the premises.

Dated:
      -------------------------     --------------------------------------------

                  NOTICE: The signature to this assignment must correspond with
                  the name as written upon the face of the within instrument in
                  every particular without alteration or enlargement, or any
                  change whatever.

Signature(s) must be guaranteed by an eligible guarantor institution
participating in a Securities Transfer Association's recognized signature
guarantee program.



                                       6