<PAGE>

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                                   FORM 10-K/A
                                 AMENDMENT NO.2

(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, 2003

  [ ]  Transition report pursuant to Section 13 or 15(d) of the Securities
       Exchange Act of 1934

                         COMMISSION FILE NUMBER 0-23383

                           OMNI ENERGY SERVICES CORP.
             (Exact name of registrant as specified in its charter)

             LOUISIANA                                   72-1395273
  (State or other jurisdiction of           (I.R.S. Employer Identification No.)
   incorporation or organization)

     4500 N.E. EVANGELINE THRUWAY                           70520
          CARENCRO, LOUISIANA                             (Zip Code)
 (Address of principal executive offices)

       Registrant's telephone number, including area code: (337) 896-6664

           Securities registered pursuant to Section 12(b) of the Act:

                                      None

           Securities registered pursuant to Section 12(g) of the Act:

                     Common Stock, $0.01 par value per share

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. Yes X No

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405
of Regulation S-K 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.___

The aggregate market value of the voting stock held by non-affiliates of the
Registrant at June 30, 2003 was $9,207,452.

The number of shares of the Registrant's common stock, $0.01 par value per
share, outstanding at May 31, 2004 was 11,393,641.

                       DOCUMENTS INCORPORATED BY REFERENCE

None.

<PAGE>
                                EXPLANATORY NOTE


On March 30, 2004, OMNI Energy Services Corp. (the "Company") filed with the
Securities and Exchange Commission (the "SEC") its Annual Report on Form 10-K
("Form 10-K") for the year ended December 31, 2003. On April 29, 2004, the
Company filed with the SEC Amendment No. 1 on Form 10-K/A ("First Amendment").
This Amendment No. 2 on Form 10-K/A corrects the language of certain
certifications to the First Amendment, properly files such certifications as
Exhibits 31.3 and 31.4 to the Form 10-K, and amends the Exhibit Index of Form
10-K to reflect these new exhibits. Except as set forth in Exhibits 31.3 and
31.4 and the Exhibit Index, the Company has not made any changes to, nor updated
any disclosures contained in its Form 10-K filed March 30, 2004, as amended by
the First Amendment.
<PAGE>

EXHIBIT INDEX

<Table>
<Caption>
            EXHIBIT NUMBER
            --------------
<S>                            <C>
                3.1            Composite Articles of Incorporation of OMNI
                               Energy Services Corp.(as of November 7, 2000).
                               (4)

                3.2            Form of Articles of Amendment -- Articles of
                               Incorporation (5)

                3.3            Bylaws of OMNI, as amended. (2)

                4.1            See Exhibit 3.1 and 3.2 for provisions of our
                               Articles of Incorporation and By-laws defining
                               the rights of holders of Common Stock.

                4.2            Specimen Common Stock Certificate. (1)

                *10.1          Form of Indemnity Agreement by and between us and
                               each of our directors and executive officers.(1)

                *10.2          Stock Incentive Plan. (1)

                *10.3          Form of Stock Option Agreements under our Stock
                               Incentive Plan. (1)

                10.4           Third Amended and Restated Loan Agreement by and
                               among us, certain of our subsidiaries and
                               Hibernia National Bank, dated October 30, 2001.
                               (3)

                21.1           Subsidiaries of OMNI Energy Services Corp. (6)

                23.1           Consent of Fitts Roberts & Co., P.C. (6)

                23.2           Consent of Ernst & Young LLP. (6)

                23.3           Notification regarding consent of Arthur Andersen
                               LLP. (6)

                31.1           Section 302 Certification of Chief Executive
                               Officer. (6)

                31.2           Section 302 Certification of Chief Financial
                               Officer. (6)

                31.3           Section 302 Certification of Chief Executive
                               Officer.

                31.4           Section 302 Certification of Chief Financial
                               Officer.

                32.1           Section 906 Certification of Chief Executive
                               Officer. (6)

                32.2           Section 906 Certification of Chief Financial
                               Officer. (6)
</Table>

----------

      *     Management contract or compensation plan or arrangement




<PAGE>
      (1)   Incorporated by reference to our Registration Statement on Form S-1
            (Registration Statement No. 333-36561).

      (2)   Incorporated by reference to our Quarterly Report on Form 10-Q for
            the quarter ended June 30, 2000.

      (3)   Incorporated by reference to our Quarterly Report on Form 10-Q for
            the quarter ended September 30, 2001.

      (4)   Incorporated by reference to our Annual Report on Form 10-K for the
            fiscal year ended December 31, 2000.

      (5)   Incorporated by reference to our Annual Report on Form 10-K for the
            fiscal year ended December 31, 2001.

      (6)   Incorporated by reference to our Annual Report on Form 10-K for the
            fiscal year ended December 31, 2003.




<PAGE>

SIGNATURES

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

                                          OMNI ENERGY SERVICES CORP.

                                          (Registrant)

                                          By:       /s/ James C. Eckert
                                              ----------------------------------
                                          James C. Eckert
                                          President and Chief Executive Officer
                                          (Principal Executive Officer)

Date:June 15, 2004

         Pursuant to the requirements of the Securities Exchange Act of 1934,
this Report has been signed below by the following persons on behalf of the
Registrant and in the capacities and on the dates indicated.

<TABLE>
<CAPTION>
             SIGNATURE                                                 TITLE                                   DATE
             ---------                                                 -----                                   ----
<S>                                            <C>                                                        <C>
        /s/ James C. Eckert                    President, Chief Executive Officer, Chairman of the        June 15, 2004
-------------------------------------------        Board
          James C. Eckert

         /s/ G. Darcy Klug                     Chief Financial Officer                                    June 15, 2004
-------------------------------------------
           G. Darcy Klug

      /s/ Deborah C. DeRouen                   Chief Accounting Officer                                   June 15, 2004
-------------------------------------------
        Deborah C. DeRouen

       /s/ Marshall G. Webb                    Director                                                   June 15, 2004
-------------------------------------------
         Marshall G. Webb

        /s/ David A. Melman                    Director                                                   June 15, 2004
-------------------------------------------
          David A. Melman

       /s/ Michael G. DeHart                   Director                                                   June 15, 2004
-------------------------------------------
         Michael G. DeHart

       /s/ Richard C. White                    Director                                                   June 15, 2004
-------------------------------------------
         Richard C. White

      /s/ Craig P. Rothwell                    Director                                                   June 15, 2004
-------------------------------------------
         Craig P. Rothwell

</TABLE>

                                       10
<PAGE>

EXHIBIT INDEX

<Table>
<Caption>
            EXHIBIT NUMBER
            --------------
<S>                            <C>
                3.1            Composite Articles of Incorporation of OMNI
                               Energy Services Corp.(as of November 7, 2000).
                               (4)

                3.2            Form of Articles of Amendment -- Articles of
                               Incorporation (5)

                3.3            Bylaws of OMNI, as amended. (2)

                4.1            See Exhibit 3.1 and 3.2 for provisions of our
                               Articles of Incorporation and By-laws defining
                               the rights of holders of Common Stock.

                4.2            Specimen Common Stock Certificate. (1)

                *10.1          Form of Indemnity Agreement by and between us and
                               each of our directors and executive officers.(1)

                *10.2          Stock Incentive Plan. (1)

                *10.3          Form of Stock Option Agreements under our Stock
                               Incentive Plan. (1)

                10.4           Third Amended and Restated Loan Agreement by and
                               among us, certain of our subsidiaries and
                               Hibernia National Bank, dated October 30, 2001.
                               (3)

                21.1           Subsidiaries of OMNI Energy Services Corp. (6)

                23.1           Consent of Fitts Roberts & Co., P.C. (6)

                23.2           Consent of Ernest & Young LLP. (6)

                23.3           Notification regarding consent of Arthur Andersen
                               LLP. (6)

                31.1           Section 302 Certification of Chief Executive
                               Officer. (6)

                31.2           Section 302 Certification of Chief Financial
                               Officer. (6)

                31.3           Section 302 Certification of Chief Executive
                               Officer.

                31.4           Section 302 Certification of Chief Financial
                               Officer.

                32.1           Section 906 Certification of Chief Executive
                               Officer. (6)

                32.2           Section 906 Certification of Chief Financial
                               Officer. (6)
</Table>

----------

      *     Management contract or compensation plan or arrangement

<PAGE>


      (1)   Incorporated by reference to our Registration Statement on Form S-1
            (Registration Statement No. 333-36561).

      (2)   Incorporated by reference to our Quarterly Report on Form 10-Q for
            the quarter ended June 30, 2000.

      (3)   Incorporated by reference to our Quarterly Report on Form 10-Q for
            the quarter ended September 30, 2001.

      (4)   Incorporated by reference to our Annual Report on Form 10-K for the
            fiscal year ended December 31, 2000.

      (5)   Incorporated by reference to our Annual Report on Form 10-K for the
            fiscal year ended December 31, 2001.

      (6)   Incorporated by reference to our Annual Report on Form 10-K for the
            fiscal year ended December 31, 2003.