The estimated cost to the Federal Savings and Loan Insurance Corp. of assisting troubled thrifts in the first five months of this year amounted to $375 million, or 140 percent more than in the comparable period last year, according to figures released yesterday. If aid continued at the same level for the rest of the year, it would total $900 million.

At a news conference called to discuss plans for helping thrifts out of their worst crisis in three decades, Federal Home Loan Bank Board Chairman Richard T. Pratt expressed confidence that FSLIC's annual cash flow of $1 billion would suffice to cover all supervisory mergers and liquidations. He also spoke optimistically about the course of interest rates and the future of S&Ls.

There have been seven involuntary mergers this year of failing thrifts and one liquidation, the first in a decade. The estimated cost to FSLIC of paying off insured depositors at Chicago's Economy Savings and Loan Association came to $60.2 million.

According to the Credit Union National Association, whose members were among the uninsured depositors, Economy had been speculating in Ginnie Mae futures, playing "interest-rate roulette." Separately this week, Rep. Benjamin Rosenthal (D-N.Y.) called on the bank board to explain why it changed accounting systems to faciliate futures trading and to supply information on associations caught speculating.

Last year FSLIC paid out $1.3 billion to acquire the assets of S&Ls it forced to merge. For the five months so far this year the only has been $577 million. However, the big difference in FSLIC's net cost of S&L mergers and liquidations is the price those assets fetch in the market in 1980 it sold the $1.3 billion in assets for $1.1 billion. This year it estimates that assets with a book value of $577 million will bring in only $202 million, hence the net $375 million cost to FSLIC.

This illustrates how much S&L assets have depreciated. Recently economist Alan Greenspan calculated that if thrifts had to liquidate their portfolios, consisting of many low-yielding mortgages, their $31 billion net worth would become a $70 billion deficit.

There are currently 265 S&Ls -- out of 4,700 in the country -- on the problem list. Although Pratt refused to specify the criteria for listing, other sources said it is a net worth of about 2-percent or less. (A net worth of zero means liabilities equal assets.) Historically, just 10 percent of those on the problem list ahve required FSLIC assistance in the course of involuntary mergers, but some economists think more will in this crisis. FSLIC insures close to $500 billion in deposits.

Pratt insisted yesterday that FSLIC assistance does not constitute a "government bailout" because the money comes from premiums paid by the S&Ls. Supervisory mergers will continue on a case-by-case basis, but another form of assistance involves capital infusions to jack up an association's net worth.

Made only infrequently in the past, capital infusions now are expected to become a key factor in the government's program to tide thrifts over until interest rates come down, a cheaper method than merger and selling off their assets at this time. Pratt noted that every one percent drop in interest rates restores $3 billion in profits to S&Ls.

Pratt said bank board legislation containing additional powers to help thrifts help themselves would be sent to Congress in about three weeks. It would give S&Ls the right to get into commercial and industrial lending and real estate investment, for example. It also would facilitate ways for mutual S&Ls to tap private capital markets.