<PAGE>

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                UNITED STATES SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

                                  FORM 10-K/A
                               (AMENDMENT NO. 1)

<Table>
<C>        <S>
(Mark One)
   [X]     ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
           SECURITIES EXCHANGE ACT OF 1934

           FOR THE FISCAL YEAR ENDED DECEMBER 31, 2002

                                  OR

   [ ]     TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
           SECURITIES EXCHANGE ACT OF 1934

           FOR THE TRANSITION PERIOD FROM          TO

                    COMMISSION FILE NUMBER 33-94884
</Table>

                          CROWLEY MARITIME CORPORATION
             (Exact name of registrant as specified in its charter)

<Table>
<S>                                                 <C>
                     DELAWARE                                           94-3148464
          (State or other jurisdiction of                            (I.R.S. Employer
          incorporation or organization)                            Identification No.)
                 155 GRAND AVENUE,                                         94612
                OAKLAND, CALIFORNIA                                     (Zip Code)
     (Address of principal executive offices)
</Table>

              REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE:
                                 (510) 251-7500

          SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:

<Table>
<Caption>
                TITLE OF EACH CLASS                      NAME OF EACH EXCHANGE ON WHICH REGISTERED
                -------------------                      -----------------------------------------
<S>                                                 <C>
                       None                                                None
</Table>

          SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT:
                     COMMON STOCK, PAR VALUE $.01 PER SHARE
                                (Title of class)

     Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. [X] Yes  [ ] No

     Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K (sec.229.405 of this chapter) is not contained herein, and
will not be contained, to the best of registrant's knowledge, in definitive
proxy or information statements incorporated by reference in Part III of this
Form 10-K or any amendment to this Form 10-K.  [ ]

     Indicate by check mark whether the registrant is an accelerated filer (as
defined in Rule 12b-2 of the Act).  [ ] Yes     [X] No

     The aggregate market value of the shares of the registrant's $0.01 par
value voting common stock held by non-affiliates of the registrant as of June
28, 2002 was $26,283,142.40 (based upon $1,258 per share being the average of
the closing bid and asked price on June 28, 2002 as reported in the Pink
Sheets). In making this calculation the issuer has assumed, without admitting
for any purpose, that all directors of the registrant are affiliates.

     As of March 17, 2003, 89,710 shares of voting common stock, $.01 par value
per share and 46,138 shares of Class N non-voting common stock, $.01 par value
per share, were outstanding.

                      DOCUMENTS INCORPORATED BY REFERENCE

     The information set forth under Part III, Items 10, 11, 12, and 13 of this
Report is, pursuant to General Instruction G(3), incorporated by reference from
the registrant's definitive proxy statement filed with the Securities and
Exchange Commission pursuant to Regulation 14A for the 2003 annual meeting of
stockholders (the "2003 Proxy Statement") that will be filed no later than 120
days after the end of the year to which this report relates.
--------------------------------------------------------------------------------
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<PAGE>

                               INTRODUCTORY NOTE

     This Amendment No. 1 on Form 10-K/A (the "Amendment") is being filed solely
for the purpose of including the certifications required by 18 U.S.C. Section
1350 as Exhibit 99.1 and Exhibit 99.2, which exhibits inadvertently set forth
the certifications required by Exchange Act Rule 13a-14 and Form 10-K. This
Amendment does not reflect events occurring after the filing of the original
Form 10-K, or modify or update the disclosures therein in any way other than as
required to provide the certifications and exhibits set forth below.

                                        2
<PAGE>

                                    PART IV

ITEM 15.  EXHIBITS, FINANCIAL STATEMENT SCHEDULES, AND REPORTS ON FORM 8-K

     (a) The following documents are filed as part of this report:

          1.  Consolidated financial statements. See Table of Contents to "Item
              8. Financial Statements and Supplementary Data" on page 39.

          2.  Consolidated financial statement schedules. See Table of Contents
              to "Item 8. Financial Statements and Supplementary Data" on page
              39.

          3.  Exhibits.

<Table>
<Caption>
           EXHIBIT
           NUMBER                            DESCRIPTION
           -------                           -----------
           <S>       <C>
            2.1      Acquisition Agreement for MTL Petrolink Corp. by and among
                     Marine Transport Corporation, as Seller, American Eagle
                     Tankers Inc. Limited, as Buyer, and Crowley Maritime
                     Corporation, as Guarantor, dated April 29, 2002**
            3.1      Certificate of Amendment of Restated Certificate of
                     Incorporation of Crowley Maritime Corporation*
            3.2      Certificate of Amendment of Restated Certificate of
                     Incorporation of Crowley Maritime Corporation*
            3.3      Restated Certificate of Incorporation of Crowley Maritime
                     Corporation*
            3.4      Restated By-Laws of Crowley Maritime Corporation*
            4.1      Form of Common Stock certificate*
           10.1      $115,000,000 Amended and Restated Credit Agreement*
           10.2      Crowley Maritime Corporation Deferred Compensation Plan as
                     amended and restated*#
           10.3      Crowley Maritime Corporation Deferred Compensation Plan
                     Trust Agreement as amended*#
           10.4      Crowley Maritime Corporation 2001 Management Incentive
                     Plan*#
           10.5      Individual Executive Benefit Agreement between Crowley
                     Maritime Corporation and James B. Rettig*#
           10.6      Split Dollar Life Insurance Agreement between Crowley
                     Maritime Corporation and Thomas B. Crowley, Jr. dated as of
                     April 1, 1992*#
           10.7      Amendment to Split Dollar Life Insurance Agreement between
                     Crowley Maritime Corporation and Thomas B. Crowley, Jr.
                     dated as of May 1, 1995*#
           10.8      Second Amendment to Split Dollar Life Insurance Agreement
                     between Crowley Maritime Corporation and Thomas B. Crowley,
                     Jr., as Trustee of the Thomas B. Crowley, Jr. Revocable
                     Trust u/t/a dtd. July 1, 1998 by and between Thomas B.
                     Crowley, Jr., as trustor and as trustee, dated as of July
                     20, 1998*#
           10.9      Split Dollar Life Insurance Agreement (1035 Exchange Policy)
                     between Crowley Maritime Corporation and Thomas B. Crowley,
                     Jr. dated as of July 20, 1998*#
           10.10     Split Dollar Life Insurance Agreement (New Policies) between
                     Crowley Maritime Corporation and Thomas B. Crowley, Jr.
                     dated as of July 20, 1998*#
           10.11     Split Dollar Life Insurance Agreement between Crowley
                     Maritime Corporation, Thomas B. Crowley, Jr. and Christine
                     S. Crowley, as Distributing Trustee of the 1998 Crowley
                     Family Generation -- Skipping Trust u/t/d dtd/ November 12,
                     1998 by and between Thomas B. Crowley, Jr., as trustor and
                     as trustee, dated as of November 24, 1998*#
           10.12     Letter Agreement and Consents regarding $115,000,000 Amended
                     and Restated Credit Agreement***
</Table>

                                        3
<PAGE>

<Table>
<Caption>
           EXHIBIT
           NUMBER                            DESCRIPTION
           -------                           -----------
           <S>       <C>
           11        Statement regarding computation of per share earnings
                     (incorporated herein by reference to Note 12 to the Crowley
                     Maritime Corporation Consolidated Financial Statements in
                     "Item 8. Financial Statements and Supplementary Data" of
                     this Registration Statement)
           21        List of all Subsidiaries****
           99.1      Certification of Chief Executive Officer pursuant to 18
                     U.S.C. Section 1350
           99.2      Certification of Chief Financial Officer pursuant to 18
                     U.S.C. Section 1350
</Table>

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

            * Incorporated by reference to the indicated exhibit to the
              Company's Registration Statement on Form 10 filed April 1, 2002.

           ** Incorporated by reference to the indicated exhibit to Amendment
              No. 1 of the Company's Registration Statement on Form 10 filed
              June 4, 2002.

          *** Incorporated by reference to the indicated exhibit to the
              Company's Form 10-Q for the quarter ended June 30, 2002.

         **** Incorporated by reference to the indicated exhibit to the
              Company's Annual Report on Form 10-K for the year ended December
              31, 2002 filed on March 19, 2003.

          # Management contract or compensatory plan or arrangement.

     (b)  Reports on Form 8-K

     No reports on Form 8-K were filed by the Registrant during the last quarter
of the fiscal year covered by this report.

                                        4
<PAGE>

                                   SIGNATURES

     Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the registrant has duly caused this report to be signed on
its behalf by the undersigned, thereunto duly authorized.

                                          CROWLEY MARITIME CORPORATION

                                          By:  /s/ THOMAS B. CROWLEY, JR.
                                            ------------------------------------
                                                   Thomas B. Crowley, Jr.
                                            Chairman of the Board, President and
                                                  Chief Executive Officer
Date: March 21, 2003

                                          By:    /s/ RICHARD L. SWINTON
                                            ------------------------------------
                                                     Richard L. Swinton
                                               Vice President, Tax and Audit
                                               (Principal Financial Officer)
Date: March 21, 2003

                                        5
<PAGE>

                                 CERTIFICATIONS

I, Thomas B. Crowley, Jr., Chairman of the Board, President and Chief Executive
Officer of Crowley Maritime Corporation, certify that:

          1.  I have reviewed this annual report on Form 10-K of Crowley
     Maritime Corporation;

          2.  Based on my knowledge, this annual report does not contain any
     untrue statement of a material fact or omit to state a material fact
     necessary to make the statements made, in light of the circumstances under
     which such statements were made, not misleading with respect to the period
     covered by this annual report;

          3.  Based on my knowledge, the financial statements, and other
     financial information included in this annual report, fairly present in all
     material respects the financial condition, results of operations and cash
     flows of the registrant as of, and for, the periods presented in this
     annual report;

          4.  The registrant's other certifying officers and I are responsible
     for establishing and maintaining disclosure controls and procedures (as
     defined in Exchange Act Rules 13a-14 and 15d-14) for the registrant and we
     have:

             a) designed such disclosure controls and procedures to ensure that
        material information relating to the registrant, including its
        consolidated subsidiaries, is made known to us by others within those
        entities, particularly during the period in which this annual report is
        being prepared;

             b) evaluated the effectiveness of the registrant's disclosure
        controls and procedures as of a date within 90 days prior to the filing
        date of this annual report (the "Evaluation Date"); and

             c) presented in this annual report our conclusions about the
        effectiveness of the disclosure controls and procedures based on our
        evaluation as of the Evaluation Date;

          5.  The registrant's other certifying officers and I have disclosed,
     based on our most recent evaluation, to the registrant's auditors and the
     audit committee of registrant's board of directors (or persons performing
     the equivalent function):

             a) all significant deficiencies in the design or operation of
        internal controls which could adversely affect the registrant's ability
        to record, process, summarize and report financial data and have
        identified for the registrant's auditors any material weaknesses in
        internal controls; and

             b) any fraud, whether or not material, that involves management or
        other employees who have a significant role in the registrant's internal
        controls; and

          6.  The registrant's other certifying officers and I have indicated in
     this annual report whether or not there were significant changes in
     internal controls or in other factors that could significantly affect
     internal controls subsequent to the date of our most recent evaluation,
     including any corrective actions with regard to significant deficiencies
     and material weaknesses.

                                              /s/ THOMAS B. CROWLEY, JR.
                                          --------------------------------------
                                                  Thomas B. Crowley, Jr.
                                                  Chairman of the Board,
                                          President and Chief Executive Officer

Date: March 21, 2003

                                        6
<PAGE>

I, Richard L. Swinton, Vice President, Tax & Audit of Crowley Maritime
Corporation, certify that:

          1.  I have reviewed this annual report on Form 10-K of Crowley
     Maritime Corporation;

          2.  Based on my knowledge, this annual report does not contain any
     untrue statement of a material fact or omit to state a material fact
     necessary to make the statements made, in light of the circumstances under
     which such statements were made, not misleading with respect to the period
     covered by this annual report;

          3.  Based on my knowledge, the financial statements, and other
     financial information included in this annual report, fairly present in all
     material respects the financial condition, results of operations and cash
     flows of the registrant as of, and for, the periods presented in this
     annual report;

          4.  The registrant's other certifying officers and I are responsible
     for establishing and maintaining disclosure controls and procedures (as
     defined in Exchange Act Rules 13a-14 and 15d-14) for the registrant and we
     have:

             a) designed such disclosure controls and procedures to ensure that
        material information relating to the registrant, including its
        consolidated subsidiaries, is made known to us by others within those
        entities, particularly during the period in which this annual report is
        being prepared;

             b) evaluated the effectiveness of the registrant's disclosure
        controls and procedures as of a date within 90 days prior to the filing
        date of this annual report (the "Evaluation Date"); and

             c) presented in this annual report our conclusions about the
        effectiveness of the disclosure controls and procedures based on our
        evaluation as of the Evaluation Date;

          5.  The registrant's other certifying officers and I have disclosed,
     based on our most recent evaluation, to the registrant's auditors and the
     audit committee of registrant's board of directors (or persons performing
     the equivalent function):

             a) all significant deficiencies in the design or operation of
        internal controls which could adversely affect the registrant's ability
        to record, process, summarize and report financial data and have
        identified for the registrant's auditors any material weaknesses in
        internal controls; and

             b) any fraud, whether or not material, that involves management or
        other employees who have a significant role in the registrant's internal
        controls; and

     6.  The registrant's other certifying officers and I have indicated in this
annual report whether or not there were significant changes in internal controls
or in other factors that could significantly affect internal controls subsequent
to the date of our most recent evaluation, including any corrective actions with
regard to significant deficiencies and material weaknesses.

                                                /s/ RICHARD L. SWINTON
                                          --------------------------------------
                                                    Richard L. Swinton
                                              Vice President, Tax and Audit

Date: March 21, 2003

                                        7
<PAGE>

<Table>
<Caption>
EXHIBIT                          EXHIBIT INDEX
NUMBER                            DESCRIPTION
-------                           -----------
<C>       <S>
     2.1  Acquisition Agreement for MTL Petrolink Corp. by and among
          Marine Transport Corporation, as Seller, American Eagle
          Tankers Inc. Limited, as Buyer, and Crowley Maritime
          Corporation, as Guarantor, dated April 29, 2002**
     3.1  Certificate of Amendment of Restated Certificate of
          Incorporation of Crowley Maritime Corporation*
     3.2  Certificate of Amendment of Restated Certificate of
          Incorporation of Crowley Maritime Corporation*
     3.3  Restated Certificate of Incorporation of Crowley Maritime
          Corporation*
     3.4  Restated By-Laws of Crowley Maritime Corporation*
     4.1  Form of Common Stock certificate*
    10.1  $115,000,000 Amended and Restated Credit Agreement*
    10.2  Crowley Maritime Corporation Deferred Compensation Plan as
          amended and restated*#
    10.3  Crowley Maritime Corporation Deferred Compensation Plan
          Trust Agreement as amended*#
    10.4  Crowley Maritime Corporation 2001 Management Incentive
          Plan*#
    10.5  Individual Executive Benefit Agreement between Crowley
          Maritime Corporation and James B. Rettig*#
    10.6  Split Dollar Life Insurance Agreement between Crowley
          Maritime Corporation and Thomas B. Crowley, Jr. dated as of
          April 1, 1992*#
    10.7  Amendment to Split Dollar Life Insurance Agreement between
          Crowley Maritime Corporation and Thomas B. Crowley, Jr.
          dated as of May 1, 1995*#
    10.8  Second Amendment to Split Dollar Life Insurance Agreement
          between Crowley Maritime Corporation and Thomas B. Crowley,
          Jr., as Trustee of the Thomas B. Crowley, Jr. Revocable
          Trust u/t/a dtd. July 1, 1998 by and between Thomas B.
          Crowley, Jr., as trustor and as trustee, dated as of July
          20, 1998*#
    10.9  Split Dollar Life Insurance Agreement (1035 Exchange Policy)
          between Crowley Maritime Corporation and Thomas B. Crowley,
          Jr. dated as of July 20, 1998*#
    10.10 Split Dollar Life Insurance Agreement (New Policies) between
          Crowley Maritime Corporation and Thomas B. Crowley, Jr.
          dated as of July 20, 1998*#
    10.11 Split Dollar Life Insurance Agreement between Crowley
          Maritime Corporation, Thomas B. Crowley, Jr. and Christine
          S. Crowley, as Distributing Trustee of the 1998 Crowley
          Family Generation -- Skipping Trust u/t/d dtd/ November 12,
          1998 by and between Thomas B. Crowley, Jr., as trustor and
          as trustee, dated as of November 24, 1998*#
    10.12 Letter Agreement and Consents regarding $115,000,000 Amended
          and Restated Credit Agreement***
    11    Statement regarding computation of per share earnings
          (incorporated herein by reference to Note 12 to the Crowley
          Maritime Corporation Consolidated Financial Statements in
          "Item 8. Financial Statements and Supplementary Data" of
          this Registration Statement)
    21    List of all Subsidiaries****
    99.1  Certification of Chief Executive Officer pursuant to 18
          U.S.C. Section 1350
    99.2  Certification of Chief Financial Officer pursuant to 18
          U.S.C. Section 1350
</Table>

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

   * Incorporated by reference to the indicated exhibit to the Company's
     Registration Statement on Form 10 filed April 1, 2002.

  ** Incorporated by reference to the indicated exhibit to Amendment No. 1 of
     the Company's Registration Statement on Form 10 filed June 4, 2002.

 *** Incorporated by reference to the indicated exhibit to the Company's Form
     10-Q for the quarter ended June 30, 2002.

**** Incorporated by reference to the indicated exhibit to the Company's annual
     report on Form 10-K for the year ended December 31, 2002 filed on March 19,
     2003.

 # Management contract or compensatory plan or arrangement.