President Ferdinand Marcos said today that he would reinstate Gen. Fabian Ver as armed forces chief of staff if Ver is acquitted of a charge of covering up the 1983 murder of opposition leader Benigno Aquino.

Ver, 64, a close confidant and cousin of Marcos, was implicated along with 24 other officers and military men and one civilian by an official fact-finding board last October. Marcos promptly replaced Ver with an acting chief of staff, and his future has remained in doubt since then. He is currently on trial with the 25 others in connection with the murder.

Marcos made the disclosure at his first news conference since June 1984. It was also one of his rare public appearances since he disappeared from the public eye in November for an extended period amid reports of serious health problems.

Marcos said today he was "recovering" from a severe virus, a bad asthma attack and other ailments. He denied that he had undergone surgery.

In response to a question, Marcos said that "there is a formal agreement among senior officers of the armed forces that if Gen. Ver is acquitted, he will be returned to his position." Marcos said this agreement was reached at a meeting in his office with commanders of all the service branches, divisions, brigades and regional unified commands. He said those present included Ver and his interim replacement,Gen. Fidel Ramos.

Marcos did not say when the meeting took place or give further details, and senior government officials professed not to know about it. Defense Minister Juan Ponce Enrile said the news conference was the first time he had heard of the meeting.

Later, at a protest rally of about 3,000 marchers near the Malacanang presidential palace, Aquino's younger brother, Agapito Aquino, said Marcos was "preparing our minds to accept his future action, the acquittal and reinstatement of Gen. Ver, no matter how unacceptable it is to the Filipino people." Aquino charged the trial was shaping up as a whitewash.

Western analysts said the reinstatement of Ver would bring a sharp reaction from Washington, which has been trying to promote reform in the Philippine military to combat a growing communist insurgency. The United States has clearly signaled Marcos that it considers Ver a hindrance to serious reforms.

The trial of Ver and the 25 other defendants formally opened Friday before three judges. Ver and seven others are accused as accessories to the murders of Aquino and Rolando Galman Aug. 21, 1983, at the Manila International Airport. The rest of the defendants are charged as principals except for the lone civilian, who is also termed an accomplice.

Defense lawyers at the current trial have been trying to get two reports by the official fact-finding board thrown out as evidence after members of the board declined to testify. The board's reports, completed in October after a year-long inquiry, form the basis of the charges against the 26 defendants.

In his news conference today, Marcos declined to comment on the trial and did not say whether he was still certain, as he said he was in 1983, that no military men were involved in the assassination of Aquino.

Marcos also asserted that the country's communist insurgency is "under firm control by the government" and denied that it was growing.

The 67-year-old president disclosed that at one point during his illness last year he had been placed in an oxygen tent "because I was hardly breathing" due to a serious asthma attack while suffering from an unspecified virus.

Today he appeared to be healthier than in recent television appearances but still well below top form. He spoke in a relatively weak, raspy voice and looked somewhat puffy about the face.