President Ferdinand Marcos' handling of a politically damaging report blaming the military for the assassination of his leading foe appears to have defused tensions here in the short term.

But further challenges lie ahead as opposition and legal groups press for punishment of those responsible and for full accountability in the case.

Marcos' move to relieve temporarily the armed forces chief of staff, Gen. Fabian Ver, and two other generals, has assuaged public opinion to some extent and won him a breathing spell, according to Western diplomats and political sources.

But the challenges already have begun, with opposition criticism of Marcos' decision to turn the case over to a government ombudsman and a civil court normally used to try low-level government officials on corruption charges.

Opposition and lawyers' groups today demanded the creation of a special, high-powered "people's tribunal" to try the 26 persons, including three top generals, named as "indictable" in a military conspiracy to kill opposition leader Benigno S. Aquino on Aug. 21, 1983.

The 26 were named in a report issued Wednesday by four members of an official fact-finding board appointed by Marcos to investigate the assassination. A dissenting report by the board's chairman accused only seven of the 26 of plotting and carrying out the killing.

In a separate development issue, the Marcos government also has come under fire for a decision by the Commission on Elections Wednesday to oust a leading opposition legislator from the new parliament, elected in May, on grounds of voting irregularities. The legislator, Aquilino Pimentel Jr., the national chairman of the opposition Pilipino-Laban Party, said today he would fight the decision, which gave his seat to his opponent from Marcos' ruling party.

The timing of the decision sparked criticism that the Marcos government was trying to bury the controversial move under the avalanche of news here about the Aquino inquiry.

Pimentel, who has been described as a future presidential contender in a post-Marcos era, has been a vocal critic of the Marcos government. He was detained last year for several months by presidential order on charges of subversion for alleged contacts with Communist insurgents.

In recent days, Pimentel also has criticized sharply President Reagan's remarks suppporting the Marcos government.

Those remarks, made during the debate with Democratic candidate Walter F. Mondale in which Reagan indicated that the only alternative to Marcos was a Communist takeover, appear to have given fresh ammunition to leftist opponents of what they call "the U.S.-Marcos dictatorship" and alienated a number of opposition moderates.

A statement by Pimentel at an anti-Marcos demonstration yesterday said: "How could Mr. Reagan come out for the continued support of a dictatorship that he saw as the sole alternative to a Communist takeover of the Philippines when that regime was driving Filipinos by the thousands into the Communist camp?

"If Mr. Reagan is not totally isolated from reality and living in the simplistic movie world of his past, he should know that the overwhelming majority of those who oppose the dictatorship are not Communists."

An open letter to Reagan issued today by the Pilipino-Laban Party condemned Reagan's "sinister barter of Filipino freedom and democracy for American protection and interest." It asked him to "reconsider your position in light of the fact that the dominant majority of the Filipino people remain opposed to all forms of totalitarianism, be it that of Mr. Marcos or the Communists."

Another open letter, addressed to the "Women of America" and signed by four Philippine women's groups, sharply denounced Reagan's statement that the alternative to Marcos was a Communist takeover.

"Nothing can be more ignorant, more uninformed, more false about what is really happening in our country today," the letter said.

It added, "We, the moderate forces who comprise the majority, have chosen to openly oppose Mr. Marcos. We are not Communists. However, we fear that, with combined U.S. support for him, a revolutionary situation will continue to develop in the Philippines which may jeopardize our option for a peaceful and democratic change."

Opposition politicians also condemned the U.S. State Department's efforts to explain Reagan's statement and mollify anti-Marcos moderates.