The chairman of the Federal Home Loan Bank Board told a congressional subcommittee yesterday that the agency's insurance arm ended 1985 with "unacceptably low" reserves of 72 cents for every $100 in customer deposits.

Chairman Edwin J. Gray, releasing the first official glimpse of the Federal Savings and Loan Insurance Corp.'s performance last year, also said that more than 15 percent of all FSLIC-insured thrifts operated at loss.

Thrift-industry officials acknowledge that the number of thrifts whose liabilities exceed their assets would reach 30 percent to 40 percent of the nation's 3,200 thrift institutions if measured by generally accepted accounting rules -- standards that are used by other industries and are tougher than the accounting rules commonly used by the thrift industry.

FSLIC insures individual deposits in savings and loan institutions for up to $100,000 each, covering almost $1 trillion in savings accounts.

During hearings of Senate and House Appropriations committees Wednesday and yesterday, Gray said that while the industry had record profits in 1985, it also had another period of "record insolvencies."

"The FSLIC fund remains under enormous strain and . . . FSLIC staff resources continue to be stretched severely," he said.

Gray said that the agency will continue to impose a special insurance premium to bolster FSLIC reserves, but he said that for a long-term solution, a substantial infusion of money is needed.

Among the most controversial plans is to help FSLIC with money obtained by an assessment on the assets of the 12 regional Home Loan Banks. The plan would require congressional approval.

Gray said that the FSLIC's primary reserves increased to $6.04 billion in 1985, up from $5.61 billion in 1984. The reserves, however, include at least $1 billion in controversial FSLIC notes, which the insurance agency has issued to failing thrifts to improve their balance sheets while a buyer is sought.

In 1984, FSLIC reserves included $700 million in the notes. The notes have been widely criticized as being, in the words of one congressman, a "creative accounting" method that props up ailing thrifts and masks the severity and extent of the industry's problems.

Even with the infusion of FSLIC notes, however, about 22 percent of the nation's federally insured S&Ls had a regulatory net worth of less than 3 percent in 1985, Gray said.

While the bank board requires S&Ls to maintain net worth equal to 3 percent of assets, the agency's beleaguered insurance fund cannot afford to close all the insolvent thrifts still in operation across the country without itself going broke.

As a result, the agency has adopted stop-gap measures to prop up net worth and defer closings while long-term solutions are sought.

Gray cautioned against the "serious impact on the FSLIC" of $2 million in potential cuts this year stemming from the Gramm-Rudmann-Hollings budget deficit act. He questioned the fairness of cutting the insurance fund, which he said is financed by the savings and loans institutions that are members of FSLIC.

In separate action yesterday, the bank board said it is considering several regulatory changes, including lifting early withdrawal penalties and limits on the number of transactions on corporate money market accounts.