A government ombudsman today took charge of the case against the Philippines' top general and 25 other persons implicated by an official fact-finding report in the assassination last year of opposition leader Benigno S. Aquino Jr., as several thousand protesters marched to demand the inclusion of President Ferdinand Marcos among the accused.

The ombudsman, Bernardo Fernandez, immediately appointed a three-member panel of prosecutors to investigate the case against the armed forces chief of staff, Gen. Fabian Ver, and two other generals, 22 military men and one civilian. The prosecutors will then decide whether those named in the report should be tried and, if so, on what charges, authorities said.

If charges are filed, trial would take place before three judges of a special nine-judge civilian court called the Sandigan Bayan, which is normally used to prosecute government officials in corruption cases.

According to Justice Minister Estelito Mendoza, the investigation by the prosecuting panel should take no longer than a month. He said the prosecutors' decision on the charges "is not reversible by anyone -- not by me and not by the president, either."

In the event of trial, the three judges of the special court must reach a unanimous verdict under the rules of the special court. Otherwise, the court must invite two of the other judges to hear the case and reach a majority decision. The final ruling can be appealed only to the Supreme Court, which is headed by a Marcos loyalist who was forced to step down as the head of an original fact-finding board in the Aquino case because of widespread skepticism about his independence.

The complicated judicial procedures and the composition of the legal bodies involved raised questions today about the impartiality and independence of the proceedings. At least one member of the newly appointed prosecutors is known for his close ties to the presidential palace.

The special civilian court, established by Marcos in a 1978 presidential decree while he ruled the country under martial law, has long had a reputation for prosecuting mostly low-level government officials and employes. Moreover, shortly before the release of the reports on Aquino's murder, Marcos appointed three new judges to the court to bring it to its full complement of nine.

Nevertheless, the head of the special court, Justice Manuel Pamaran, insisted that the judges were independent. He said he doubted that Marcos would try to influence the case "because he respects the judiciary."

Foreign Minister Arturo Tolentino, who is known as something of a maverick within the government, also said the special court was independent.

But a western diplomat said, "There are very strong signals that this whole thing is orchestrated." He added, "I think Marcos did what he had to do immediately to relieve the pressure, but I find all this very contrived."

He cited a letter Marcos sent to Ver to grant Ver's request for a "temporary leave of absence" after Ver was implicated in a military conspiracy to assassinate Aquino by four members of the board. A dissenting report by board chairman Corazon Agrava specifically absolved Ver and accused only seven military men, including a general, in a "criminal plot" against the opposition leader. Aquino was assassinated Aug. 21, 1983, seconds after he arrived at Manila International Airport following three years of self-imposed exile.

Marcos' letter to Ver called the majority report's findings "shocking" and criticized both the board's investigation and the "so-called evidence" it produced against the general, a long-time confidant and trusted associate of Marcos.

In his letter to Ver, Marcos wrote, "The circumstances under which the board has chosen to implicate you in its findings are fraught with doubt and great contradictions of opinion and testimony." Marcos expressed confidence that "the rigors of judicial process will ferret out the truth and arrive at justice."

Further doubts about eventual action on the findings by the board's majority were expressed by Agapito Aquino, the younger brother of the slain opposition leader.

"After people have time to reflect, they will realize that things are still the same," he said. The ombudsman's office and the special court, he said, "are all creations of Marcos." He said he feared the case could become "tied up in the legal process, with a lot of delays."

Aquino spoke as he led about 5,000 antigovernment demonstrators in a march to protest the board's failure to implicate Marcos along with the 26 others accused in his brother's murder.

Also participating were Aquino's widow, Corazon, and former senator Lorenzo Tanada, 86, the patriarch of the anti-Marcos opposition.

Among the placards carried by the marchers was one that said, "Gen. Ver: Are you trying to save your master?" Another said, "Board's verdict: military conspiracy. People's verdict: U.S.-Marcos conspiracy." One placard bore a picture of Agrava, the author of the dissenting report, with the inscription: "I couldn't scare less."

Opposition leader Tanada said the majority report was of "historic importance," although "it may not be complete because it does not involve directly President Marcos." He told the crowd that Marcos had issued statements constituting involvement in a cover-up, notably one in which he denied categorically shortly after the assassination that any members of his government were involved.