President Ferdinand Marcos accepted a dissenting report today on the assassination of opposition leader Benigno S. Aquino Jr. after a fact-finding board investigating his killing failed to resolve differences over the extent of the military conspiracy in the case.

Corazon Agrava, the chairwoman of the panel, presented a copy of her report on the assassination to Marcos at Malacanang Palace. Neither Marcos nor Agrava revealed any details of her findings. Marcos, in accepting the report, said the case would be prosecuted before a special court "because military men are involved."

The other four members of the board were preparing to issue a separate report representing a majority opinion.

Comments from other panel members had indicated that Agrava disagreed with their decision to accuse the armed forces chief of staff, Gen. Fabian Ver, of involvement in the Aug. 21, 1983, killing of Aquino.

Aquino, 50, was shot once in the head seconds after leaving a plane in the custody of military guards at the Manila International Airport.

The military blamed the assassination on Rolando Galman, 33, a small-time hoodlum allegedly hired for the job by Communist rebels. Galman was killed at scene by the military guards, and his body lay on the tarmac for several hours before it was removed.

Agrava was to release her report to the media later today. An earlier statement by the chairwoman, distributed to more than 100 reporters awaiting the panel's report in a hallway outside the board's offices, was the first public acknowledgement of a split among the five members who conducted a 10-month investigation.

There was no immediate response from the other panelists -- businessman Dante Santos, 59; labor leader Ernesto Herrera, 43; educator Amado Dizon, 75, and corporate lawyer Luciano Salazar, 65. None was at the board offices when Agrava, 69, issued the announcement.

In returning home after three years of self-exile in the United States, Aquino had ignored warnings from the government, including one delivered personally by the president's wife, Imelda Marcos, that he risked assassination by unidentified plotters if he came back to the Philippines.

His return, aimed at uniting the badly divided political opposition to Marcos, came at a time when the president was reported seriously ill and there were rumors in both government and opposition circles that he was dying. Western diplomats said senior government and military officials evidently perceived Aquino's return as a bid to engineer his own succession to Marcos.

The whole sequence of events left little doubt among most Filipinos from the beginning that Aquino was killed by military men and that Galman was set up to take the blame. But the boards's efforts to establish this turned out to be a long and tedious process.

In recent weeks, Marcos has sought to disassociate himself from the original military claim, which he endorsed publicly and promoted, that Aquino was shot by Galman on behalf of Communist rebels. Marcos also has repeated his intention to abide by the recommendations of the fact-finding board and said anyone responsible would face prosecution.