<PAGE>   1
                                                                     EXHIBIT 3.A


                                    RESTATED

                          CERTIFICATE OF INCORPORATION

                                       OF

                           EL PASO NATURAL GAS COMPANY

                     Pursuant to Sections 242 and 245 of the
                General Corporation Law of the State of Delaware

         E1 Paso Natural Gas Company, a corporation organized and existing under
the laws of the State of Delaware, hereby certifies as follows:

         1. The name of the corporation is E1 Paso Natural Gas Company (the
"Corporation"). The Corporation was originally incorporated under the name E1
Paso Natural Gas Company. The original certificate of incorporation was filed
with the Secretary of State of the State of Delaware on November 28, 1928.

         2. This Restated Certificate of Incorporation restates and further
amends the Certificate of Incorporation of the Corporation and has been adopted
and approved in accordance with Sections 242 and 245 of the General Corporation
Law of the State of Delaware. Stockholder approval of this Restated Certificate
of Incorporation was given by unanimous written consent of the stockholders of
the Corporation in accordance with Section 228 of the General Corporation Law of
the State of Delaware.

         3. The text of the Certificate of Incorporation, as heretofore amended,
is hereby amended and restated to read in its entirety as follows:


                                    ARTICLE 1
                                      NAME

          The name of this corporation is El Paso Natural Gas Company.


                                    ARTICLE 2
                           REGISTERED OFFICE AND AGENT

         The address of the registered office of this corporation is Corporation
Trust Center, 1209 Orange Street, City of Wilmington, County of New Castle,
State of Delaware 19801, and the name of its registered agent at such address is
The Corporation Trust Company.
<PAGE>   2

                                    ARTICLE 3
                                    PURPOSES

         The purpose of this corporation is to engage in any lawful act or
activity for which corporations may be organized under the General Corporation
Law of the State of Delaware.


                                    ARTICLE 4
                                     SHARES

         The total number of authorized shares of all classes of stock of this
corporation shall consist of 1,000 shares of common stock having a par value of
$1.00 per share and 1,000,000 shares of preferred stock having a par value of
$0.01 per share. Authority is hereby expressly granted to the Board of Directors
to fix by resolution or resolutions any of the designations and the powers,
preferences and rights, and the qualifications, limitations or restrictions
which are permitted by the General Corporation Law of the State of Delaware in
respect of any class or classes of stock or any series of any class of stock of
the corporation.

PREFERRED STOCK DESIGNATED "8% PREFERRED STOCK"
-----------------------------------------------

         Pursuant to the authority vested in the Board of Directors of the
Corporation by the Certificate of Incorporation, as amended (as such may be
further amended from time to time, the "Certificate of Incorporation"), a series
of Preferred Stock, par value $0.01 per share, of the Corporation (the
"Preferred Stock") be, and hereby is, created to be designated "8% Preferred
Stock" (hereinafter referred to as the "8% Preferred Stock"), consisting of
500,000 shares, and the designations, powers, preferences and relative and other
special rights and the qualifications, limitations and restrictions of the 8%
Preferred Stock are hereby fixed and stated to be as follows (all terms used
herein that are defined in the Certificate of Incorporation shall be deemed to
have the meanings provided therein):

                  SECTION 1. Dividends. (a) The dividend rate on the 8%
         Preferred Stock shall be 8% of $700 per share of Preferred Stock per
         annum. Dividends on shares of the 8% Preferred Stock shall be
         cumulative and shall accrue from the date of issuance of such shares,
         whether or not declared by the Board of Directors of the Corporation
         (or a duly authorized committee thereof). Accrued but unpaid dividends 
         shall not bear interest.

                  (b) Dividends on the 8% Preferred Stock shall be payable when,
         as, and if declared by the Board of Directors of the Corporation (or a
         duly authorized committee thereof) out of assets legally available
         therefor, annually on the last day of November in each year (each, a
         "Dividend Payment Date"), with the first dividend payment date being
         the next Dividend Payment Date following the date of issuance.
         Dividends on each Dividend Payment Date will be payable to holders


                                      -2-
<PAGE>   3

         of record of the 8% Preferred Stock as they appear on the records of
         the Corporation on a record date, not more than 60 days preceding such
         Dividend Payment Date, fixed for such purpose by the Board of Directors
         (or a duly authorized committee thereof) in advance of such Dividend
         Payment Date. Accrued dividends not paid on a Dividend Payment Date may
         be declared and paid at any time, without reference to any regular
         Dividend Payment Date, to the holders of record on such record date,
         not more than 60 days preceding the payment date thereof, as may be
         fixed by the Board of Directors (or a duly authorized committee
         thereof). Dividends payable on shares of 8% Preferred Stock for the
         initial dividend period following issuance of such shares or any other
         dividend period shorter than a year shall be computed on the basis of a
         360-day year of twelve 30-day months. The 8% Preferred Stock shall rank
         on a parity with each other series of Preferred Stock as to the payment
         of dividends, except to the extent otherwise provided in the resolution
         or resolutions of the Board of Directors of the Corporation fixing the
         designations and the powers, preferences, and rights, and the
         qualifications, limitations, and restrictions in respect of such other
         series of Preferred Stock.

                  SECTION 2. Voting. The 8% Preferred Stock shall not have any
         voting rights except as required by law or the Certificate of
         Incorporation.

                  SECTION 3. Redemption. (a) At any time or from time to time,
         on or after January 1, 2003, the shares of the 8% Preferred Stock shall
         be redeemable at the option of the corporation (by resolution of the
         Board of Directors or a duly authorized committee thereof), in whole or
         in part, out of funds legally available therefor, at a redemption price
         equal to $700.00 per share, plus an amount equal to all accrued and
         unpaid dividends, if any, to but excluding the date fixed for
         redemption. If fewer than all outstanding shares of 8% Preferred Stock
         are to be redeemed, the Corporation will select those shares to be
         redeemed pro rata, by lot, or by a substantially equivalent method.

                  (b) Notice of redemption pursuant to paragraph (a) of this
         Section 3 shall be given by mail, not less than 30 days prior to the
         date fixed for redemption, to each record holder of the shares of 8%
         Preferred Stock to be redeemed at the address of such holder on the
         records of the Corporation. If a notice of redemption has been given
         pursuant to this subsection (b) and if, on or before the date fixed for
         redemption, the funds necessary for such redemption shall have been
         irrevocably deposited or set aside by the Corporation, separate and
         apart from its other funds, to pay the redemption price to the holders
         of the shares of 8% Preferred Stock so called for redemption upon
         surrender of the certificates therefor, then, notwithstanding that any
         certificates for such shares have not been surrendered for
         cancellation, from and after the date fixed for redemption, dividends
         on the shares of 8% Preferred Stock so called for redemption will cease
         to accrue, such shares will no longer be deemed outstanding, and all
         rights of the holders thereof as stockholders of the Corporation
         (except the right to receive 


                                      -3-
<PAGE>   4

         payment of the redemption price) will cease. Subject to applicable
         escheat and similar abandoned property laws, any moneys so deposited or
         set aside by the Corporation for such redemption and unclaimed at the
         end of six months from the date fixed for redemption shall revert to
         the general funds of the Corporation, after which reversion the holders
         of such shares so called for redemption shall look only to the general
         funds of the Corporation for payment of the amounts payable upon such
         redemption. Any interest accrued on funds so deposited or set aside
         shall be paid to the Corporation from time to time.

                  SECTION 4. Liquidation Rights. (a) The shares of 8% Preferred
         Stock shall rank, as to distributions upon dissolution, liquidation,
         and winding up of the Corporation, prior to the shares of Common Stock
         and on parity with each other series of Preferred Stock, except to the
         extent otherwise provided in the resolution or resolutions of the Board
         of Directors of the Corporation fixing the designations and the powers,
         preferences, and rights, and the qualifications, limitations, and
         restrictions in respect of such other series of Preferred Stock.
         Subject to subsection (b) of this Section 4, the amount that the
         holders of 8% Preferred Stock shall be entitled to receive in the event
         of any dissolution, liquidation, or winding up of the affairs of the
         Corporation, whether voluntary or involuntary, shall be $700.00 per
         share, plus an amount equal to all accrued and unpaid dividends, if
         any, to the date of dissolution or liquidation. After such amount is
         paid in full, no further distributions or payments shall be made in
         respect of shares of 8% Preferred Stock, such shares of 8% Preferred
         Stock shall no longer be deemed to be outstanding or be entitled to any
         powers, preferences, rights, or privileges, and certificates
         representing such shares of 8% Preferred Stock shall be surrendered for
         cancellation to the Corporation.

                  (b) In the event of any dissolution, liquidation, or winding
         up of the Corporation, then, before any distribution or payment shall
         be made to the holders of Common Stock or any other class or series of
         stock of the Corporation ranking junior to the 8% Preferred Stock with
         respect to distributions upon dissolution, liquidation, or winding up,
         the holders of the 8% Preferred Stock (subject to the rights of the
         holders of any class or series of stock ranking prior to the 8%
         Preferred Stock with respect to distributions upon dissolution,
         liquidation, or winding up) shall be entitled to be paid in full the
         amounts set forth in subsection (a) of this Section 4. After such
         payment shall have been made in full to the holders of the 8% Preferred
         Stock, the remaining assets and funds of the Corporation shall be
         distributed to the holders of the stock of the Corporation ranking
         junior to the 8% Preferred Stock with respect to distributions upon
         dissolution, liquidation, or winding up according to their respective
         rights. In the event that the assets of the Corporation available for
         distribution to the holders of 8% Preferred Stock shall not be
         sufficient to pay in full the preferential payment herein required to
         be paid to the holders of shares of 8% Preferred Stock and to pay in
         full the liquidation preference on all other shares of stock of the
         Corporation ranking on parity with the 8% Preferred Stock with respect
         to


                                      -4-
<PAGE>   5

         distributions upon dissolution, liquidation, and winding up of the
         Corporation, then such assets shall be distributed to the holders of
         shares of 8% Preferred Stock and any such other parity stock ratably in
         proportion to the full amounts to which they otherwise would be
         respectively entitled if all amounts payable thereon were paid in full.

                  SECTION 5. Maturity. Unless otherwise redeemed as provided
         herein, the term of the 8% Preferred Stock shall be perpetual.


                                    ARTICLE 5
                                     BY-LAWS

         The Board of Directors shall have the power to adopt, amend or repeal
the By-laws of this corporation, subject to the power of the stockholders to
amend or repeal such By-laws. The stockholders having voting power shall also
have the power to adopt, amend or repeal the By-laws of this corporation.


                                    ARTICLE 6
                              ELECTION OF DIRECTORS

         Except as may be otherwise required by the By-laws, written ballots are
not required in the election of Directors.


                                    ARTICLE 7
                    INDEMNIFICATION OF OFFICERS AND DIRECTORS

         The Corporation shall indemnify its officers and directors to the full
extent permitted by the General Corporation Law of the State of Delaware, as
amended from time to time.


                                    ARTICLE 8
                        LIMITATION OF DIRECTOR LIABILITY

         No director of the Corporation shall be personally liable to the
Corporation or its stockholders for monetary damages for breach of fiduciary
duty as a director, for any act or omission, except that a director may be
liable (i) for breach of the director's duty of loyalty to the Corporation or
its stockholders, (ii) for acts or omissions not in good faith or that involve
intentional misconduct or a knowing violation of law, (iii) under Section 174 of
the General Corporation Law of the State of Delaware, or (iv) for any
transaction from which the director derived an improper personal benefit. If the
General Corporation Law of the State of Delaware is amended to authorize
corporate action further eliminating or limiting the personal liability of
directors, then the liability of the directors shall be eliminated or limited to
the fullest extent 


                                      -5-
<PAGE>   6

permitted by the General Corporation Law of the State of Delaware, as so
amended. The elimination and limitation of liability provided herein shall
continue after a director has ceased to occupy such position as to acts or
omissions occurring during such director's term or terms of office. Any
amendment, repeal or modification of this Article 8 shall not adversely affect
any right of protection of a director of the Corporation existing at the time of
such repeal or modification.

         IN WITNESS WHEREOF, the undersigned has caused this Restated
Certificate of Incorporation to be executed by a duly authorized officer this
11th day of May 1999.


                                        El Paso Natural Gas Company


                                                /s/ JEFFREY I. BEASON
                                        ----------------------------------------
                                                    Jeffrey I. Beason
                                               Vice President and Controller



                                      -6-