The Federal Housing Administration suffered another multibillion-dollar loss in 1989, and its books are in such poor shape that the loss may be even worse, government auditors said Friday.

"As we projected last year, FHA's financial condition has significantly worsened," the General Accounting Office said in a letter to the House and Senate banking committees.The FHA's mortgage insurance program lost $3.9 billion in the fiscal year ending Sept. 30, 1989, the latest period for which financial information is available, said the GAO, Congress' watchdog agency. The FHA lost $4.2 billion in 1988.

The program, at the end of the 1989 fiscal year, backed $329 billion in mortgages, including $251 billion in low-down-payment single-family loans.

"There are indications that losses have continued in 1990 and will continue in 1991," GAO Assistant Comptroller General Donald H. Chapin wrote.

The bulk of the 1989 loss, $3.5 billion, came in the FHA's General Insurance Fund, which insures apartment construction loans, property improvement loans, cooperative and condominium mortgages and other specialized loans. The far larger Mutual Mortgage Insurance (MMI) Fund insures single-family home loans.

Unlike the MMI fund, the GI fund is not necessarily intended to operate without a loss.

Chapin cautioned that FHA's accounting systems are so weak that it is difficult to determine the severity of the loss. Nevertheless, he said the FHA was $6.7 billion in the red at the end of 1989.

The Department of Housing and Urban Development, which oversees the FHA, has identified changes needed to shore up its funds, but it has failed to implement most of them, the GAO said.

"Although some of these steps have been carried out, it is apparent from the report that real progress has been slow and

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that more forceful actions are needed now. Full implementation of corrective actions will almost certainly reduce the continuing losses at FHA," Chapin wrote.

"In the meantime, the problems continue and losses are often not detected until months after they occur," he wrote. "For example, because FHA's delinquency tracking system contains inaccurate, incomplete and late data, FHA may not know that a default has occurred for up to nine to 12 months after the loan has begun to show problems."

Mary Brunette, a HUD assistant secretary, said steps have been taken to stem the losses in both the MMI and GI funds.

"We recognize there are enormous problems in the FHA. They developed over a long period of time and all the solutions are not instantaneous. But we think progress has been made and we think the next report will be much better," she said.