A New Jersey company that built two incinerator ships to burn toxic wastes at sea with the help of the Maritime Administration has defaulted on its federally backed loans, costing the taxpayers $64 million.

The default is the latest setback for the maritime agency, which provided the loan guarantees as part of a controversial construction subsidy program that has been overwhelmed by a record-breaking wave of ship bankruptcies. In the last three years, the bankruptcies have cost the Maritime Administration $650 million.

At Sea Inc., the New Jersey company that owns the incinerator ships, defaulted on its payments last week, in part because it failed to obtain the necessary permits from the Environmental Protection Agency and thus was unable to use the ships. At Sea's corporate parent, Tacoma Boatbuilding Co. of Tacoma, Wash., filed for Chapter 11 bankruptcy protection in September, the latest victim of a depression in the U.S. shipbuilding industry.

With the newest defaults, the maritime agency has borrowed $281 million from the Treasury Department since July, when its reserve fund for ships built with federal loan guarantees ran dry.

Samuel B. Nemirow, a former maritime administrator who represents At Sea, said the company itself has not filed for bankruptcy. But, he said, "They're not paying their bills." No one was answering the phones at At Sea's New Jersey office yesterday, which Nemirow acknowledged was "not a good sign."

"This is a case of shortsightedness of astounding proportions," Washington maritime lawyer Allan I. Mendelsohn said. "The Maritime Administration never should have been in the business of financing millions of dollars for ships when they didn't know anything about the environmental hazards or the business they were getting into . . . . They ought to fire the whole Maritime Administration."

The agency is beginning foreclosure proceedings on the ships, the Apollo I and II, which are nearly complete. But because of a quirk in the bankruptcy laws, the agency must vie with other creditors during several years of litigation before it can take control of the ships. Even then, the ships cannot be operated until the EPA approves the new technology.

EPA officials issued an experimental permit yesterday for two incinerator ships owned by At Sea's chief rival, Chemical Waste Management of Oak Brook, Ill. They said they also were prepared to approve At Sea's application, filed last summer, had the company not run into financial trouble.

But after three years of regulatory delays and heated objections from communities near the proposed test sites, At Sea finally ran out of money.

The two companies adopted differing strategies in their race to control what is expected to be a lucrative market in disposing of PCBs and other hazardous wastes. At Sea's ships obtained federal backing in 1982 under the Maritime Administration's Title 11 program, which guarantees bonds for American-built ships. Chemical Waste could not receive such subsidies because its ships were built abroad, where construction costs are far lower than in U.S. shipyards.

Former maritime administrator Harold E. Shear lobbied hard for the ships that his agency had subsidized. He urged the EPA to reject permits for Chemical Waste in favor of the American-built ships, and tried to convince the Defense Department to use the vessels for waste disposal.

Maritime Administration officials defended the ships amid growing criticism that their 47-year-old subsidy program was making too many shaky investments. Edmund Fitzgerald, a senior agency official, said early last year that the incinerator ships were only "a moderate risk." And last spring, the agency increased At Sea's $55 million loan guarantee by $17 million, although the full amount was not used.

The agency originally believed that At Sea had enough money and enough time to win EPA approval, a spokesman said yesterday. "As events have unfolded," he said, "the amount of capital needed was greater than projected and . . . the permitting process took longer than anticipated."

At Sea spokesmen said earlier this year that they had received a $20 million infusion from new investors and could ride out any further delays. But when At Sea missed its debt service payment last week, the trustee for the ships' bond holders, National Bank of Washington, demanded that the maritime agency pay off the bonds.

From 1970 to 1982, the agency guaranteed $10 billion in ship construction loans, or 10 times as much as it had in the program's previous 32 years. Its reserve fund was virtually depleted in June when it had to absorb a record $135 million default on two refurbished cargo ships run by Houston ship operator C.C. Wei.