The whereabouts of Nicaraguan guerrilla leader Eden Pastora was in doubt today after his rebel force reported that he was missing after his helicopter went down yesterday afternoon in southeastern Nicaragua.

The wreckage of a helicopter thought to be that of Pastora was found 12 miles inside Costa Rica tonight, but police said they found no trace of its occupants.

Two media reports indicated that Pastora had managed to escape to Panama in a second aircraft. One of them, a Costa Rican radio station, said he was recovering from slight injuries. The Nicaraguan Defense Ministry said the reports of a disappearance were a publicity stunt to raise money.

These claims were denied by a spokesman for Pastora's Democratic Revolutionary Alliance, known by its Spanish initials ARDE, who was contacted by telephone in San Jose.

"He is not in Panama. We have people out looking for him in the jungle right now," said the ARDE spokesman. He added that Pastora had disappeared yesterday afternoon during a trip to inspect guerrilla outposts inside Nicaragua. The pilot of Pastora's Hughes helicopter reported by radio that he was having mechanical trouble, and then contact was lost with the aircraft, the spokesman said. He added that troops of the Sandinista government were patrolling in the area.

The Associated Press, however, quoted a cousin of Pastora as saying the guerrilla leader had been flown to Panama in a second helicopter after his aircraft went down. The cousin, Hector Dario Pastora, is public relations director for a political organization that works with ARDE.

Costa Rica's Radio Monumental also reported that Pastora was safe in Panama after suffering "slight" injuries in the downing of the helicopter. The radio station did not cite a source for the report.

Nicaragua's Defense Ministry issued a communique questioning reports that Pastora was missing.

"It is a new show by the traitor Pastora, with the intention of appearing in the news of the world, on television and in the written press, to obtain more money from the CIA," the statement said.

Pastora is one of the most famous of the rebels battling the Sandinistas because he was a well-known Sandinista commander in the insurrection that toppled dictator Anastasio Somoza in 1979. Pastora was named deputy defense minister after the revolution, but he broke with his former comrades in 1981 and left the country because of dissatisfaction over the government's close relations with Soviet Bloc nations and other issues.