Almost 15,000 District of Columbia homeowners will have to pay higher than necessary real estate taxes this fall unless they file an affidavit with the city by Monday, the D.C. Finance and Revenue Department warned yesterday.

The affidavits qualify owner-occupants of homes or condominiums for a tax exemption on $9,000 of each dwelling's value, which saves about $120, depending upon what tax rate is set. This year, for the first time, the affidavits also qualify homeowners for a lower tax rate.

There are an estimated 65,000 owner-occupants in the city.

Although the finance department sought to encourage filing by making a separate mailing of the affidavit forms to citizens, about 11,000 fewer have filed them this year than the 61,000 who did in 1978, according to Kenneth Back, department director.

Last year the department enclosed the blank forms in envelopes containing assessment notices. Many citizens complained that they overlooked the affidavits.

Under an emergency measure passed by the City Council and signed into law yesterday by Mayor Marion Barry, only homes for which affidavits have been filed will qualify for the lower of two residential tax rates. Others will be taxed as rental property at a somewhat higher rate, not yet set, that the new law authorizes. A thrid, higher rate will be levied on commercial property.

Back said affidavits may be obtained and filed with the department's assessment services division in the Municipal Center, 300 Indiana Ave. NW. Telephone information numbers are 727-6410 and 727-6440.