<Page>

                                                             Exhibit 99.906.Cert

FORM N-CSR ITEM 10(b) EXHIBIT

                            CERTIFICATION PURSUANT TO
                             18 U.S.C. SECTION 1350,
                             AS ADOPTED PURSUANT TO
                  SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002

        The undersigned hereby certify in their capacity as Treasurer and
President, respectively, of EATON VANCE MUTUAL FUNDS TRUST (the "Trust") (on
behalf of Eaton Vance Tax-Managed Equity Asset Allocation Fund), that:

  (a)  the Annual Report of the Trust (on behalf of Eaton Vance Tax-Managed
       Equity Asset Allocation Fund) on Form N-CSR for the period ended
       October 31, 2003 (the "Report") fully complies with the requirements
       of Section 13(a) or 15(d) of the Securities Exchange Act of 1934, as
       amended; and

  (b)  the information contained in the Report fairly presents, in all
       material respects, the financial condition and the results of operations
       of the Trust (on behalf of Eaton Vance Tax-Managed Equity Asset
       Allocation Fund) for such period.

A SIGNED ORIGINAL OF THIS WRITTEN STATEMENT REQUIRED BY SECTION 906 HAS BEEN
PROVIDED TO THE TRUST AND WILL BE RETAINED BY THE TRUST AND FURNISHED TO THE
SECURITIES AND EXCHANGE COMMISSION OR ITS STAFF UPON REQUEST.

EATON VANCE MUTUAL FUNDS TRUST (On behalf of Eaton Vance Tax-Managed Equity
Asset Allocation Fund)

Date:  December 16, 2003
       -----------------


/S/ James L. O'Connor
- ---------------------
James L. O'Connor
Treasurer

Date: DECEMBER 16, 2003


/S/ Thomas E. Faust Jr.
- -----------------------
Thomas E. Faust Jr.
President