The Reagan administration yesterday indirectly criticized the acquittal of Gen. Fabian C. Ver and 24 other Philippine military men in the 1983 assassination of Philippine opposition leader Benigno Aquino, saying the verdict was "very difficult to reconcile" with evidence implicating the military in the murder.

State Department spokesman Charles Redman also said Ver's reappointment as chief of the Philippine armed forces raised doubts about President Ferdinand Marcos' commitment to his "professed desire to initiate serious reforms" in the military.

While administration officials stopped short of saying the decision might jeopardize U.S. aid to the Philippines, Rep. Stephen J. Solarz (D-N.Y.), chairman of the House Asia subcommittee, immediately called for a suspension of military aid "as long as Gen. Ver remains as chief of staff of the armed forces."

It was not clear what action the administration or Congress might, or could, take in regard to U.S. assistance to the Marcos government without jeopardizing strategic U.S. military bases at Clark Air Field and Subic Bay. The bulk of U.S. aid is in a five-year, $900 million package of economic support and military assistance tied to the U.S. military bases agreement with the Philippines.

In the Republican-controlled Senate, an aide to Sen. Richard G. Lugar (R-Ind.), chairman of the Foreign Relations Committee, predicted that Ver's acquittal and reinstatement would raise "serious doubts about the direction of our aid."

The aide, Mark Helmke, said Lugar was planning to hold hearings on the Philippines next week, at which time the committee's reaction to the Ver decision would become clearer. Already, the "general mood" within the committee was that the needed military reforms were "questionable" under Ver's leadership, he said. In a statement, Lugar said "the court ruling does not contribute to the crying need for credibility in the Philippines government."

Sen. Paul Laxalt (R-Nev.), who earlier this fall served as a presidential envoy to Marcos, said the verdict had come "as no great surprise" and that he had warned the Philippine president that Ver's reinstatement would provoke criticism in the United States. Echoing the administration, Laxalt added that repercussions in Washington would be shaped by the "length and circumstance" of Ver's reinstatement.

Redman said it was very difficult to reconcile "the exemplary, thorough work" of the investigation carried out in 1984 by the panel known as the Agrava Board, which unanimously refuted the government's contention that a lone communist gunman, Rolando Galman, had shot Aquino.

The five-member board, appointed by Marcos himself and headed by retired appeals court justice Corazon Agrava, found the murder to be the work of Philippine military personnel, who were subsequently charged with both the crime and a cover-up. While four of the members implicated Ver, Agrava concluded he was not involved.

Redman reiterated the administration position that those responsible for the Aquino murder, "no matter who they may be," be punished "to the fullest extent of the law."

"The key issue at this juncture," Redman said, "is the perception of the Philippine people as to whether justice has been done. Only the Filipinos themselves can make that determination."

The Marcos government regards most U.S. aid as "rent" for the bases, but the administration has taken the position that at least $475 million in economic support funds is "aid" and its disbursal tied to "adequate progress" on policy reform.

Congressional Democrats have recently sought to cut back the military assistance portion of the package. But Pentagon officials have argued that any cuts in military funds only reduce U.S. leverage over the Philippine armed forces.