The Maritime Administration, which has been subsidizing the American shipbuilding industry for half a century, soon may be hit with a series of major bankruptcies that could require an emergency bailout from the U.S. Treasury for the first time.

The owners of two ships, the Jade Phoenix and Golden Phoenix, missed mortgage payments this month on $128 million in ship construction debts guaranteed by the Maritime agency. If the payments aren't made by May 1, the loans will be in default and the agency will have to repay the creditors.

Such a default would be the largest in the agency's history, a costly and embarrassing end to the agency's long struggle to salvage the ships.

The agency had launched an elaborate plan to rebuild the vessels after discovering that thousands of insulation cracks had rendered them useless. But the rebuilt ships have been in financial straits, and agency officials recently tried to sell them to the Navy.

In another case, the Maritime Administration arranged for a series of paper companies to take over four abandoned tankers that now are close to a $219 million default. Despite the agency's efforts, the tankers have been sitting idle for years at ports in Virginia and Rhode Island.

Jesse Calhoon, president of the National Marine Engineers Beneficial Association, said he has been warning for a year "that this was a disaster waiting to happen, and now it has happened. It's going to destroy the whole program. . . . The problem is gross neglect and mismanagement."

The Title 11 loan guarantees are one of an array of federal subsidies designed to support a domestic shipbuilding industry that has been unable to compete in the world marketplace. Under the program, the government guarantees bonds sold to finance ship construction.

But a slump in world shipping and a depressed oil industry have produced an unprecedented 438 defaults over the last three years, forcing the agency to pay off $222 million in loans.

The Maritime Administration has $141 million left in a reserve fund to cover more than $7 billion in outstanding loan guarantees under the Title 11 program. But the Office of Management and Budget, anticipating that the fund may be wiped out, has set aside $200 million this year to pay off the loans.

"They're about to have some big defaults," OMB spokesman Edwin L. Dale Jr. said of the maritime agency. "We just know they're coming." He said the agency made "so many bad commitments" because it was "too loose" in financing risky ventures.

If the income-producing reserve fund is depleted, it would be the first time in the 47-year history of the Title 11 ship construction program that the agency would have to borrow money from the Treasury.

At a time when every domestic spending program is under severe scrutiny by budget cutters, the administration may face an unavoidable increase in maritime outlays.

The issue is a sensitive one for the Transportation Department agency. Neither Maritime Administrator Harold E. Shear nor his top deputies would comment on the rising tide of defaults.

But agency spokesmen say the program is a sound attempt to bolster an aging U.S.-flag fleet. It has fallen on hard times, they add, because of the global slowdown in shipping, which some experts now estimate has idled half the world's shipping capacity.

Many of the recent defaults involve tugs, barges and crewboats that were idled by the downturn in offshore oil drilling, agency spokesman Walter Oates said.

Oates said the agency recently adopted "more stringent guidelines" that require applicants to increase their investment in each ship, pay higher loan fees and better document their chances of success. He said that shipbuilders will be required to do "some pretty good homework in terms of convincing the agency that this is a viable project."

The program sailed along at a modest level until the last decade. From 1970 to 1982, the Maritime Administration issued $10 billion in loan guarantees, or 10 times the amount approved in the previous 32 years. New guarantees dwindled to $177 million last year because of the shipping slump.

As previous loans have gone sour, the agency has dipped into the fund to avert still more defaults. It has made $10 million in debt service payments over the past year for eight companies that couldn't meet their obligations.

The program's finances have become so shaky that the House Merchant Marine and Fisheries Committee, normally a sympathetic forum, has begun an investigation of the Title 11 program.

"We've always been concerned that an agency responsible for promoting shipbuilding is the same agency that is acting as the banker on loans to shipbuilders," a congressional aide said. "There's the seeds of a conflict of interest."

The result is that some of the agency's largest loan guarantees are coming under new scrutiny. For example:

* The Phoenix ships have missed two debt payments in the last two years, but avoided default when the Maritime agency came up with $9.2 million from the reserve fund. The ships missed another payment this month and face default when a 30-day grace period expires May 1.

Agency officials won't say whether they plan to pay that $9.1 million installment or absorb the $128 million default that might follow.

The Phoenix saga dates to 1969, when the El Paso Co. contracted for three tankers to import liquid natural gas from Algeria. The tankers were virtually finished in 1979 at a cost of more than $300 million, including $52 million in direct government outlays and the remainder in federally insured loans.

But inspections revealed thousands of tiny cracks in the insulation, rendering the ships useless for carrying natural gas.

In 1980 Lloyd's of London agreed to pay $300 million in an unprecedented insurance settlement, and $210 million was placed in a security fund to pay off the project's bondholders.

The matter might have ended there. But Houston ship operator C. C. Wei approached the government with an ambitious plan to convert the tankers to bulk carriers that could haul coal, grain and other dry cargo.

Shear approved the plan in 1981, giving Wei use of the insurance money and federally backed financing. The repairs were made in a South Korean shipyard by the architectural firm headed by John J. McMullen. Shear had worked for another company owned by McMullen before joining the agency, but a government ethics review found nothing improper in his actions.

Days after the plan was approved, one of the ships, the Columbia, ran aground in a storm and was damaged beyond repair. The government had to use one-third of the $210 million security fund to pay bondholders; the balance has been spent on the other two ships.

Those ships can lose money even when they carry cargo. They are too large to be accommodated by many world ports, and often load only to half capacity.

The ships have found some work under the Food for Peace program, which by law reserves half its shipments for U.S.-flag vessels. They have spent about half the last year ferrying grain to Africa and Asia.

But the debt-laden ships apparently remain in financial trouble, for Shear has spent months trying to convince the Navy to buy them. Ironically, this would require yet another multimillion-dollar conversion to make the ships suitable for the Navy's reserve fleet, and Navy officials have refused.

A representative of Wei's Houston-based firm, Falcon Shipping Group, said company officials were in "intense negotiations" and would have no comment.

Former Maritime administrator Robert Blackwell, who has represented Wei, did not return phone calls.

There is one more twist to the Phoenix tale: The vessels also serve as a tax shelter. Atlantic Richfield Co. purchased the tax benefits on the two ships in 1981 under President Reagan's now-defunct safe-harbor leasing program.

In exchange for a payment to Wei's company, Arco now deducts millions of dollars from its federal taxes for depreciation and investment in the two ships. An Arco official said the tax breaks could end if the ships went bankrupt.

* Four liquid natural gas tankers that were abandoned by their original owner are edging closer to a $219 million default.

The idle ships are owned by GEN Marine Co. Inc., a holding company with no real assets that is named for a former maritime agency official. It, in turn, is owned by two other companies created by the U.S. Corporation Co., which is in the business of setting up paper companies.

The Maritime Administration arranged for this chain of holding companies to take title to the ships and is paying $1.4 million a year for their upkeep.

El Paso Co. turned over the four tankers to the Maritime agency in 1983 in a $12 million settlement when planned contracts to import natural gas failed to materialize. The agency has tried in vain to find work for three of the ships; the other is the storm-damaged Columbia.

The agency has used the $90 million in insurance money from the Columbia's accident to pay debt service on the ships, but that fund has dwindled to $18.3 million. Another $15.5 million is due by May 15, and the following installment next fall could trigger a default.

* The owner of two incinerator ships, which are being built with a $55 million loan guarantee, recently persuaded the Maritime agency to approve an additional $17 million in federally backed financing.

Maritime officials acknowledge that the ships, Apollo I and II, cannot find work until the Environmental Protection Agency grants them a permit to burn hazardous wastes at sea. Their owner, At Sea Inc., is about to apply for an EPA research permit for one ship to make an experimental burn, the first step in a lengthy approval process.

With the federal guarantee at stake, Shear has pressed the EPA to grant the permits.

But an EPA spokesman said the issue is so controversial that no commercial permits will be issued this year. In fact, EPA approval of commercial permits for the only two competing ships, owned by Chemical Waste Management Inc., has been delayed for years.

Now the Apollo ships face an unlikely complication: the sperm whale.

The EPA spokesman said the burn site that was planned for At Sea off the New Jersey coast is in jeopardy because officials have discovered it is in the migratory path of the endangered whale. He added that there is "enormous public resistance" to the other likely incineration site in the Gulf of Mexico.

An At Sea representative called the whale issue "a red herring" and said the ships will use any site approved by EPA. He said At Sea is in strong shape thanks to a $20 million cash infusion from a firm that took over its ailing parent company, Tacoma Boatbuilding Co.

The At Sea spokesman said the extra federal financing will be used for new safety equipment to satisfy objections from environmentalists and prove that the technology is safe.

"Stringing us out on the permit process does not sound the death knell on our project," he said. "We are prepared to ride out the delays. We'll roll the dice on the quality of our ships."