Calling the mounting losses at savings institutions a "national problem," New York state's top banking regulator, Muriel Siebert, urged formation of a presidential commission to consider the future of the thrift industry.

Siebert, state superintendent of banks, said today the commission should consist of the secretaries of Treasury, Commerce, and Housing and Urban Development and be charged with long-range planning to replace what she termed the "stop-gap and short-term remedial steps taken so far at the federal level."

Siebert proposed the commission at a news conference at which she announced that operating losses at New York state-chartered savings banks reached $372 million during the third quarter, 23 percent more than in the second quarter. Total operating losses for the first three quarters of 1981 in New York state amount to $897 million.

Siebert remarked that many people think the "thrift problem" is a "New York City problem" because losses have been far greater here than elsewhere. To prove it is a national problem, she cited Federal Savings & Loan Insurance Corp. figures showing that thrift institutions in 49 out of 50 states had aggregate net operating losses in the first six months of this year.

Sixty-nine percent of the savings and loans nationwide showed such losses, she said, and since June that figure has risen to about 80 percent. And there have been 18 mergers this year requiring FSLIC assistance.

The idea of a presidential commission received a lukewarm reception. Sen. Jake Garn (R-Utah), whose banking committee is considering a comprehensive bill, commented, "We've had adequate studies, and we know what to do on short and long term. What we need now is more action and not more studies." William B. O'Connell, executive vice president of the U.S. League of Savings Associations, which is holding its annual convention here, said he doubted a presidential commission would do anything beyond what the Congress is now doing. Moreover, he added that what the troubled thrift industry needs now is less rather than more visibility and publicity while it works out its problems.

Figures released yesterday indicate that 97 out of 105 New York state-chartered savings banks had operating losses last quarter. These include Bowery Savings Bank, with a $42.1 milllion loss; Dime, $29.1 million; Dry Dock $19.6 million; Emigrant, $22.6 million; Greenwich (which was merged recently into Metropolitan) $20.9 million, the Metropolitan $5.1 million; New York Bank for Savings, $34.5 million; Seaman's, $13.6 million and Union Dime, $11.6 million.

The aggregate net worth of all New York state savings banks fell to $4.4 billion, or 17 percent less than it was at the end of 1980. Siebert declined to say how many more mergers will occur in New York this year but said that every bank in the state will be solvent throughout the year.

In California Siebert reported 130 savings and loans had losses of over $273 million in the first half of this year; in Florida 77 S&Ls lost $85 million and in Texas 216 S&Ls lost more than $100 million.