The federal government transferred a record number of federal properties to local governmental units last year for use as low- and moderate-income housing. Now the small discount conveyance program faces an uncertain future.

The program was begun in 1969 to help communities and local nonprofit groups develop housing for disadvantaged or handicapped families.

In its first 13 years, just seven federal properties were transferred, but in 1982 five more parcels--most of them abandoned Air Force housing units--were made available.

But officials at both the Department of Housing and Urban Development and the General Services Administration now say they are not certain that the program will be allowed to continue beyond fiscal 1983. And, at the end of this month, its functions will be transferred from HUD's New Communities Development Corp. to the Office of the Federal Housing Commissioner.

"We may be here, and we may not," said Angelo Scioscia, director of the surplus land and housing office. "It's a political decision that is now being made." Scioscia said he only learned Wednesday morning that his troops would be transferred to another part of HUD.

The disposal of federal property at less than fair market value for low- and moderate-income housing is one of several discount conveyance programs now in operation, affecting parks, educational and health sites, airports, historic-monument sites and highways. The other transfers, unlike the housing conveyances, are made at no cost to the recipients.

"There are relatively few requests for low- and moderate-income housing units because the program is not that well known," said James Crammond, a staff assistant in HUD's surplus lands division."

Because of tighter budgets brought on by hard economic times,"More communities are looking everywhere for housing," Crammond said. There is "a little more emphasis because of the housing shortage."

The program is run by HUD, but GSA handles the negotiations and makes the properties--unwanted by other federal agencies--available to local housing groups through HUD on a selective basis. When GSA has a property that may be best suited for use as low- or moderate-income housing, it lets HUD know, and then HUD must find a buyer--at "fair value for use" as housing--according to Earl C. Jones, GSA's assistant commissioner for real property.

Although the transfers have been few and infrequent, they often become controversial.

Currently, for example, political leaders in New York and Long Island are squabbling over the sale of the old Montauk Air Force Base radar station, fearing the property would be overdeveloped. Part of that property, supposed to be used by the Town of East Hampton as low- and moderate-income housing, is snagged in the dispute over how the surrounding 282 acres of the old station should be used.

And just across the Golden Gate Bridge from San Francisco, the Marin County Redevelopment Authority and the GSA scrapped over whether the nonprofit Ecumenical Association for Housing could have 18 acres of the old Hamilton Air Force Base.

In that case, local GSA officials--abiding by the new Reagan administration policy to sell, rather than give away, federal lands--told GSA officials in Washington that they wanted to kill the deal (according to Freedom of Information Act documents obtained by the Independent-Journal, a Marin County newspaper). San Francisco GSA officials said the tract could become "a high-quality business park." GSA officials here eventually disagreed, allowing the transfer for $1.5 million.