<PAGE>   1
                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                    FORM 10-Q


                                Amendment No. 1


    (Mark One)
[X]  QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES
     EXCHANGE ACT OF 1934

                  For the quarterly period ended March 31, 1999

                                       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 No. 0-22483
                         -------

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

                            SEVEN SEAS PETROLEUM INC.
             (Exact name of registrant as specified in its charter)

     YUKON TERRITORY                                     73-1468669
     (State or other jurisdiction of                     (I.R.S. Employer
     incorporation or organization)                      Identification No.)

     SUITE 1700 5555 SAN FELIPE HOUSTON, TEXAS           77056
     (Address of principal executive offices)            (Zip Code)

     Registrant's telephone number, including area code: (713) 622-8218

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

     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 the number of shares outstanding of each of the issuer's classes
of common stock, as of the latest practicable date.

AS OF APRIL 30, 1998 THERE WERE 37,833,420 SHARES OF THE REGISTRANT'S COMMON
SHARES, NO PAR VALUE PER SHARE, OUTSTANDING.


<PAGE>   2
             SEVEN SEAS PETROLEUM INC. AND SUBSIDIARIES
                  (A Development Stage Enterprise)
               STATEMENTS OF CONSOLIDATED CASH FLOWS
                           (In thousands)


<TABLE>
<CAPTION>
                                                                                                             Cumulative
                                                                                                             Total from
                                                                                                              inception
                                                                                                             February 3,
                                                                          Three Months Ended March 31,         1995) to
                                                                         ------------------------------       March 31,
                                                                             1999               1998             1999
                                                                         ------------      ------------      ------------
<S>                                                                      <C>               <C>               <C>
OPERATING ACTIVITIES
     Net loss                                                            $     (1,104)     $     (1,115)     $   (103,546)
     Add (subtract) items not requiring (providing) cash:
     Compensation expense                                                          --                --             2,140
     Minority interest                                                           (113)              (78)           (1,249)
     Common stock contribution to 401(k) retirement plan                           --                --                79
     Depreciation and amortization                                                255                84             1,231
     Writedown of proved oil & gas properties                                      --                --           129,789
     Gain on sale of exploration properties                                        --                --              (546)
     Dry hole and abandonment costs                                                --                --             1,140
     Gain on sale of marketable securities                                         --                (6)               (6)
     Deferred income taxes benefit                                                 --                --           (45,727)
     Amortization of discount on investments                                       41                --                41
     Changes in working capital excluding changes to cash and
       cash equivalents:
        Accounts receivable                                                    (1,372)             (478)           (7,052)
        Interest receivable                                                       123                --              (409)
        Inventory                                                                  27                --            (1,289)
        Prepaids and other, net                                                    71                 9              (154)
        Accounts payable                                                       (2,856)             (427)            2,854
       Other accrued liabilities                                                  (46)              (92)              533
                                                                         ------------      ------------      ------------
Cash Flow Used in Operating Activities                                         (4,974)           (2,103)          (22,171)
                                                                         ------------      ------------      ------------

INVESTING ACTIVITIES
     Exploration of oil and gas properties                                     (8,379)           (9,746)          (80,724)
     Purchase of land                                                             (21)             (441)           (1,278)
     Purchase of investments                                                       --                --           (38,301)
     Proceeds from acquisition                                                     --                --               630
     Proceeds from sale of property                                                --                --             1,247
     Proceeds from sale of marketable securities                                   --                50                50
     Note receivable from related party                                            --                --              (200)
     Other asset additions                                                       (140)              (47)           (1,896)
                                                                         ------------      ------------      ------------
Cash Flow Used in Investing Activities                                         (8,540)          (10,184)         (120,472)
                                                                         ------------      ------------      ------------

FINANCING ACTIVITIES
     Proceeds from special warrants issued                                         --                --            12,393
     Proceeds from share capital issued                                            --             1,116            15,466
     Proceeds from additional paid-in capital contributed                          --                --                 1
     Proceeds from issuance of  long-term debt                                     --                --           135,000
     Costs of issuing long-term debt                                               --                --            (5,821)
     Contributions by minority interest                                         1,378             1,829            11,615
                                                                         ------------      ------------      ------------
Cash Flow Provided by Financing Activities                                      1,378             2,945           168,654
                                                                         ------------      ------------      ------------

NET INCREASE (DECREASE) IN CASH AND CASH EQUIVALENTS                          (12,136)           (9,342)           26,011
Cash and cash equivalents, beginning of period                                 38,147            18,067                --
                                                                         ------------      ------------      ------------
CASH AND CASH EQUIVALENTS, END OF PERIOD                                 $     26,011      $      8,725      $     26,011
                                                                         ============      ============      ============
</TABLE>


Supplemental disclosures of cash flow information:

The Company incurred interest costs of $3.4 million for the three month period
   ended March 31, 1999 and $9.8 million for the year ended December 31, 1998.
   Such amounts were capitalized during the respective periods.

Cash paid for interest for the three month period ended March 31, 1999 and for
   the year ended December 31, 1998 was zero and $8.1 million, respectively.

The Company paid zero for estimated income taxes during the three months ended
   March 31, 1999.


   The accompanying notes are an integral part of these financial statements.

                                       4
<PAGE>   3

but not in part, at any time at a redemption price equal to 100% of the
principal amount thereof plus accrued and unpaid interest, liquidated damages
and additional amounts, if any, to the redemption date in the event of certain
changes affecting withholding taxes applicable to certain payments on the Senior
Notes. Upon the occurrence of a change of control, (i) unless the Company
redeems the Senior Notes as provided in clause (ii) below, the Company will be
required to offer to purchase the Senior Notes at a purchase price equal to 101%
of the aggregate principal amount thereof, plus accrued and unpaid interest,
liquidated damages and additional amounts, if any, to the date of purchase, and
(ii) the Company will have the option, at any time prior to May 15, 2002, to
redeem the Senior Notes, in whole but not in part at a redemption price equal to
100% of the principal amount thereof plus the applicable premium and accrued and
unpaid interest, liquidated damages and additional amounts, if any, to the date
of redemption.

    The Senior Notes are senior obligations of the Company and rank pari passu
in right and priority of payment with all existing and future senior
indebtedness of the Company.


    Colombia. In 1995, the Company acquired a 15% interest in the Dindal and Rio
Seco Association Contracts through its participation in El Segundo 1-E, the
Guaduas Field discovery well. In 1996, the Company acquired an additional 36.7%
in the Dindal and Rio Seco Association Contracts in Colombia in exchange for the
issuance of the Company's common shares valued at $153.1 million in the
aggregate at that time. In 1997, the Company acquired an additional 6% in the
Dindal and Rio Seco Association Contracts in Colombia in exchange for the
issuance of the Company's common shares valued at $18.6 million in the aggregate
at that time. From inception through March 31, 1999, the Company had cash
expenditures for the acquisition, exploration, and development of its oil and
gas properties of $80.7 million.


    The Company's estimated capital expenditures assume in each case that each
of the associates in the Association Contracts approves and pays its
proportionate share of capital expenditures. Under the terms of the Association
Contracts, if a commercially feasible discovery is made, the Colombian national
oil company ("Ecopetrol") may acquire a 50% interest in the property, and the
interests of all other parties to the contract, including the Company, will be
reduced by 50%. Ecopetrol will bear 50% of the associated development costs and
will reimburse the other associates for 50% of certain exploration activities.
The Association Contracts require Ecopetrol's participation in the production
facilities. The Company expects that Ecopetrol will participate to the extent of
50% of the pipeline and infrastructure costs. No assurances can be given,
however, that an agreement will be reached on these terms and the Company may be
required to fund amounts greater than the amounts presented as the Company's net
share. Ecopetrol retains the right not to participate initially in the
development. In this case, the associates can develop the Guaduas Field under a
sole risk provision, and will be required to invest 100% of the development
costs. After the associates have recovered 200% of the costs invested for
development plus 50% of certain exploration costs, Ecopetrol will become a
participant in the project at a 50% interest.

    Total 1999 capital expenditures on the Company's non-operated Tapir
Association Contract area are estimated to be $0.6 million. Such expenditures
will be made to complete the Mateguafa 1 well, which was drilled in 1998, and to
drill the Caporal 1 exploratory well on the block. The Caporal 1 well was
plugged and abandoned in April 1999.

    To date, all oil revenues have been due to the Company's share of crude oil
produced during production testing of the Company's wells on the Guaduas Field.
Although the Company intends to continue to sell oil resulting from production
tests, significant commercial production is not expected until further
development of the field through the drilling, well operations and construction
of production and pipeline transportation facilities. The Company has completed
plans for the construction of pipeline and production facilities at the Guaduas
Field. Permitting and the purchasing of equipment and supplies for pipeline and
production facilities is in process. Anticipated completion of Increment II at
20,000 Bbls/d to 30,000 Bbls/d is year-end 2000.

    The Company plans to conduct seismic operations on the Montecristo and
Rosablanca Association Contract areas in 1999 for an estimated cost of $2.5
million. The Company is considering acquisition of outside funding via farm-out
or forming an alliance with a seismic contractor to complete this work. Either
of these events will result in a reduction of the Company's interest.

    Australia. The Company is in the process of eliminating any mandatory
capital commitments outside of Colombia. In the Bass Strait Basin offshore
southeast Australia, the Company is seeking to farm out its interests. If the
Company does not farm-out its interests in this prospect and an exploratory well
is drilled during 1999, the Company will have an estimated $2.2 million capital
commitment for this prospect during 1999.

    In 1998, the Company completed the sale of its 11.77% working interest in
the Perth Basin in Western Australia for approximately $0.9 million in cash and
the reimbursement of approximately $0.3 million for certain capital
expenditures.


                                       10
<PAGE>   4

    As the Company develops its infrastructure at the Guaduas Field, it will
continue to monitor Year 2000 compliance issues as they relate to equipment
supplied by its vendors and contractors. Since the Company does not currently
supply significant oil production to its customers, and no supply contracts have
been entered into in respect of the Guaduas Field production, the Company is
unable to assess the significance of Year 2000 issues affecting potential
customers at this stage in its operations.

ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURE ABOUT MARKET RISK

    Seven Seas is exposed to market risk, including adverse changes in commodity
prices, interest rates and foreign currency exchange rates as discussed below.

    Commodity Risk. The Company's exposure in the commodity pricing applicable
to its oil and natural gas production is currently minimal due to the small
amounts of oil and gas produced to date. Realized commodity prices received for
such production are primarily driven by the prevailing worldwide price for crude
oil and spot prices applicable to natural gas. The effects of such pricing are
expected to be minor until such time as the Company produces commercial
quantities of oil and gas.

    Interest Rate Risk. The Company considers its interest rate risk exposure to
be minimal as a result of a fixed interest rate on the $110 million 12 1/2%
Senior Notes. The Company currently has no open interest rate swaps agreements.

    Foreign Currency Exchange Rate Risk. The Company conducts business in
several foreign currencies and is subject to foreign currency exchange rate risk
on cash flows related to sales, expenses and capital expenditures. However,
because predominately all transactions in Seven Seas' existing foreign
operations are denominated in U.S. dollars, the U.S. dollar is the functional
currency for all operations. Exposure from transactions in currencies other than
the U.S. dollars is not material.


PART II. OTHER INFORMATION

Item 6.  Exhibits and Reports on 8-K

    (a) Exhibits

    27 Financial Data Schedule

    (b) Reports on From 8-K

    None

    SIGNATURES

    Seven Seas Petroleum Inc. Date:


    April 13, 2000              By:  Larry A. Ray Executive Vice President,
                                Chief Operating Officer and Chief Financial
                                Officer

                                Sir Mark Thomson, Bt.
                                President


                                       13