An American, missing for more than a year after a yacht trip off Southeast Asia, was reported yesterday to have been held in a Cambodian prison under the deposed regime of Pol Pot and confessed to being a CIA spy.

The French news agency, Agence France-Presse, said in a dispatch from the Cambodian capital Phnom Penh that the name of a U.S. citizen, James William Clark, appeared in prison records pertaining to 44 foreigners held in a Phnom Penh jail up to last November.

Another missing American, Len McNamara, was named in a deposition found among the prison records, but it was unclear whether he had ever been held in Cambodia. His fate also was unknown.

The report quoted one of seven "surviving prisoners" at the Toul Sleng jail as saying the foreigners had been taken away to an unknown destination by Khmer Rouge soldiers and were never seen again. This evidently occurred on the eve of the Vietnamese invasion that deposed the Communist government of Khmer Rouge leader Pol Pot and installed a pro-Hanoi Communist administration.

The AFP dispatch cited a 20-page deposition found among the prison records in which Clark allegedly confessed he was "on a spy mission" when he, McNamara and a third man were captured aboard a boat on April 21, 1978 by the Cambodian coast guard near Poulo Way Island in Cambodian territorial waters.

In the deposition, AFP said Clark listed his "CIA registration number" as 1,492.

The reports prompted efforts by the U.S. State Department to clear up the mystery shrouding the fate of the two Americans.

A State Department statement yesterday said, "We have tentatively identified these men as having been on a yacht reported missing in May, 1978." It added that the government is "urgently seeking further information" and has approached the Cambodian delegation at the United Nations in New York and the Vietnamese embassy in Paris.

The State Department said it could not give any other information about the two men because of the U.S.Privacy Act and that it had no previous reports of their presence in Cambodia.

A State Department spokeswoman said relatives of McNamara had contacted the department last May and said they had not heard from him in a year. Subsequent inquiries to U.S. Embassies in Asia produced no information on his whereabouts, the spokeswoman said.

The Central Intelligence Agency, citing its policy, refused to confirm or deny whether Clark was one of its agents and referred inquiries about any U.S. prisoners in Cambodia to the State Department.

The report from Phnom Penh said there was no information available to show whether Clark and fellow foreign prisoners were now dead or alive. It said they were last seen in November 1978 when they were being transferred from Toul Sleng prison and that the new Cambodian authorities have not reported discovering the bodies of any non-Asians since coming to power.

The AFP correspondent, Jean-Pierre Gallois, said it was evident that no serious investigation had yet been conducted by the new Cambodian authorities.But he quoted a prison official as saying that documents recovered would be examined "soon" and would probably reveal more details about the identity and fate of the prisoners.

Washington sources held out little hope that many of the prisoners could have survived their ordeal. Hundreds of thousands of Cambodians are believed to have died in the previous government's purges and during its efforts to force city dwellers to move into the countryside.

Thousands more died during the warfare and famines that have plagued Cambodia for the past decade. Survivors now are threatened by severe food shortages that have prompted the new authorities to seek international aid.

The AFP report said Clark's alleged confession, transcribed in the deposition into the Cambodian language, described how he had been recruited by the CIA in November, 1974. The document said Clark was introduced to recruiters by a man he met while serving time in a California prison together from 1969 to 1971 for refusing military service.

Among the Cambodian prison records, AFP said, were several photographs of white men.

One of them showed three men on the deck of a ship, two of them wearing diving paraphenalia. Another photo showed one of the men posing aboard a yacht with an elderly couple who could have been his parents.

According to the alleged deposition, Clark had worked on yacht repairs at a boatyard in Santa Barbar, California.

The document listed the names, transcribed phonetically into Khmer, of relatives living in california and Hawaii.