An agency of the General Assembly, saying state government must spend at least $172 million to cover losses in Maryland's savings and loan crisis, reinforced today Gov. Harry Hughes' strategy of gradually solving the problem by spending government money and selling assets of crippled thrift associations.

In its first detailed analysis of the financial debacle that has dominated the state since last May, the Department of Fiscal Services sharply disagreed with Hughes' estimate of how much money the state can recover through civil lawsuits as it tries to end the crisis by 1990.

The department also disputed the governor's estimate of the cost of repaying the 50,000 depositors of Old Court Savings & Loan of Baltimore.

However, the thrust of the 34-page report bolstered key elements of Hughes' plan to end the crisis, including the partial repayment of Old Court depositors with $100 million in transportation funds and another $70 million in general government funds.

The expenditure of $100 million from the transportation trust fund has drawn sharp criticism from suburban legislators who fear they will lose money for badly needed road improvements.

Today, though, after reviewing the report by the Fiscal Services Department, the leadership of the state Senate and House of Delegates embraced Hughes' plan to spend the transportation funds as a first step to ending the savings and loan crisis.

"This report brings the House, the Senate and the executive together," said Senate President Melvin A. Steinberg (D-Baltimore County). "The basic plan is set."

Benjamin L. Cardin, the speaker of the House of Delegates, also predicted that the legislature will make no major changes in Hughes' depositor relief plan. "We have to present a unified position to the bond houses" that have been reviewing Maryland's coveted AAA bond rating, Cardin said.

The fiscal services estimate of a $172 million overall loss in the thrift crisis corresponds to figures used by Hughes in preparing his budget for the coming year.

The report listed nine scenarios Maryland officials could face in the months ahead as they grapple with the sale of Old Court assets and the planned sale of Community and First Maryland savings and loans.

Federal officials have yet to approve the sales of those two Montgomery County thrifts, and many legislators fear that one or both of the deals may fall through.

If that happens, the state government may still be selling off the assets of Community and First Maryland as late as 1991 and 1993, respectively, the Fiscal Services Department said.

Hughes, who hopes the federal government will approve the Community and First Maryland sales, has made a separate pledge of $164 million in state funds to persuade prospective buyers to take on the two ailing thrifts. The governor's plan assumes that the state will be able to recover more than $70 million of that sum through the sale of the thrifts' assets and repayment of loans.

In the case of Old Court, the Hughes administration has estimated it will cost the state an initial $124.8 million to pay back depositors by 1990, with a recovery of at least $75 million of that through civil litigation.

The fiscal services department disputed both of those projections, saying its "moderate" estimate calls for a $133.8 million cost and its "pessimistic" estimate a $154.7 million cost.

William S. Ratchford II, director of the Fiscal Services Department, also said the projected $75 million recovery through civil lawsuits was too speculative an estimate.

"There is not any basis for making a firm estimate" of dollars to be recovered in some future legal action, he said.

Also today, Rep. Barbara Mikulski (D-Md.) introduced legislation in Congress to grant tax relief to Maryland savings and loan depositors whose accounts have been frozen. The bill would exempt federal income taxes on interest earned on savings accounts, if depositors cannot withdraw the interest because of the bankruptcy or insolvency of the financial institution.

Taxes would have to be paid once depositors have access to the interest income.