With the noise of New Years still echoing across San Diego's dark harbor, the first big tuna boats began slipping away from the dock early today to open what could be the final season for the huge U.S. tuna fishing industry.

Owners of the boats - sleek giants that each run 200 or more feet in length and cost upwards of $5 million - are warning that they will shift flags and government solves the problem of porpoises killed during the tuna fishing.

Such a shift, according to industry experts, could virtually end the $180 million-a-year U.S. tuna fishing industry.

Most of the commerical tuna fishing is done from here. The total dollar value of the catch amounts to nearly 30 per cent of all the fin fish caught by U.S. boats.

Tuna industry spokesman say it is likely that more than 1,000 crewmen who work on the boats would lose their jobs if there is a shift to foreign flags. In addition there would be cutbacks in tuna packing plants, many of which are located in this area.

Since tuna boat owners have begun making it known they might shift flags, at least eight years of big tuna boats have taken the first step toward formally changing to foreign registries. Dozens of other companies are considering the shift, industry sources say.

Representatives from other countries have been coming here seeking to sign up members of the U.S. tuna fleet.

The fleet is generally regarded as the best equipped and most proficient among international tuna fleets. Representatives from Mexico, Peru, Costa Rica, Panama and a number of other tuna fishing countries have been in contact, tuna industry spokesmen said.

The controversy stems from the fact that porpoises are mammals and drown when they get trapped in the nets of fishermen seeking yellowfin tuna, the species most of the boats here hunt.

The 1972 Marine Mammal Protection Act, passed after complaints from conservationists that tuna fleets were destroying porpoise schools, grant the National Marine Fisheries Service the right to set limits on the annual size of the porposie kills. Last year the fisheries service allowed kills of 78,000 porpoises, a figure that U.S. tuna fisherman complained was unreasonably low and based on scanty data.When the total was reached Oct. 15 the yellowfin season was cut off for U.S. fishing boats working the Pacific tuna grounds off the central and South American coasts.

No new quaot has been approved although the fisheries service has recommended that U.S. boats be allowed to kill 29, 920 porposies before cutting off the yellowish season.

Last week U.S. District Court Judge Charles R. Richey in Washington rejected a joint appeal by the American Tunaboat Association, the industry trade association, and the fisheries service to grant U.S. fishermen a temporary yellow fin permit until April 30.

The effect of the judge's ruling has been to leave the approximately 138 boats of the U.S. tuna fleet without permission to hunt yellowfin while foreign flag tuna boats were free to begin hunting the fish as of midnight Jan. 1 under international treaty.

Unless the porpoise question is settled soon or a temporary permit is issued, U.S. tuna fisherman say the yellow fin will be filled by foreign boats.

"The whole thing is a doomsday situation," said Augusta Felando, general manager of the tunaboat association. "It throws the whole fishing program we've all worked on out of whack," he said.

Manuel Vangas, owner of the 196-foot tuna Saratoga said: "It's like a conspiracy to drive us out of the country."

Like most tuna boat owners, Vargas has an investment of several million dollars in his vessel. Last week he filled out an application to shift its registry from the U.S. to Venezuela.

Altering the registry of a commercial boat like Vargas' is not a simple procedure. An application must be filed with the U.S. Maritime Administration and an arrangement must be made with the foreign country to register the boat there.

Manuel Silva, head of the Tunaboat Association and owner of two fishing boats, said he consulted with representatives from Peru and Mexico last week about shifting the boats' registry. To do it, he said, would probably require finding a buyer from one of those countries willing to put up nearly $7 million for the boats, or joining a foreign-controlled corporation that would own the vessels.

"It's hard to believe this is happening," said Silva, 46, a member of one of several large Portuguese families which own many of the giant tuna boats docked here. "But you can't let an investment like that rot at the dock. If I have to move to Mexico for a couple of years, you bet I'll do it."

It costs about $7,000 a day in lost income and expenses while awaiting a final decision on the porpoise problem and Silva, like most boat owners here, said his craft would be leaving for the yellow fin fishing area in the next couple of days with or without a permit.

"We'll pray for some kind of miracle in the courts or in Congress here at home," Silva said. "But sometimes, when you're way out there at sea with no one around, it's like coming to a stop light in the middle of the desert. No one's there to watch so you just don't pay much attention to the rules."