The Reagan administration sent an unusually strong public signal yesterday to Philippine President Ferdinand C. Marcos about the clouded future of that country's top military officer, who is suspected of complicity in the murder of opposition leader Benigno S. Aquino Jr.

State Department spokesman John Hughes, reading from a prepared statement, took note of the "swift action" of Marcos yesterday in ordering prosecution of seven military men named in the report of the chairman of a five-member commission that investigated the slaying.

Hughes declared, "We expect that the Philippine government will take equally swift action following the submission of the majority report, which we understand will be issued tomorrow. We trust that, as President Marcos has promised, those responsible for Sen. Aquino's murder, no matter who they may be, will be held accountable for this terrible crime."

Though cloaked in polite diplomatic language, the statement's unmistakable and intended target was Gen. Fabian C. Ver, the armed forces chief of staff and longstanding close associate of Marcos. Ver is widely reported to be implicated in the Aquino assassination by the four commission members whose report is to be submitted to Marcos today.

By calling for "equally swift action" against those responsible for the killing, "no matter who they may be," the U.S. statement was a public appeal to Marcos to move against his old and well-placed friend.

Officials said the statement was worded to foreclose any possibility that Marcos might give credence only to the report of the commission chairman, Corazon Agrava, who did not name Ver. The State Department, the officials noted, referred to the conclusions of the four other commission members as "the majority report."

Administration sources said there was no clear indication what action Marcos will take when confronted with the commission majority's accusations of a widespread military conspiracy extending to the level of the top uniformed military man in the Philippines.

"This is an unusually difficult situation for Marcos," an administration official said.

He added, in a view shared throughout U.S. policy-making ranks, that Marcos' handling of the accusations will be "of great importance" in indicating the extent to which he is serious in dealing with the Aquino assassination and the deepening political conflict that followed.

Concern about the situation in the Philippines and Marcos' ability to deal with it effectively has been building for many months in official Washington. "Nobody is in a mood to shore up Marcos," said an official, noting coolly that "maybe he Marcos can hack it, and maybe he can't."

The tone of such comments. which are notably skeptical of Marcos, seemed at variance with President Reagan's remarks in Sunday night's presidential debate that "we're better off" backing Marcos and his government "rather than throwing them to the wolves and then facing a communist power across the Pacific."

Some officials reacted with dismay to Reagan's off-the-cuff remarks, which seemed to suggest no alternative between the rule of Marcos and a communist takeover. Softening statements backing "other forces working for democratic change" were made Monday at the State Department.

Officials in the State and Defense departments denied a published report of a rift within the administration over how serious the Philippine situation is and how strongly Marcos should be confronted about his internal problems. Policy makers in both departments appeared seriously concerned as the Manila situation approached what they described as a new turning point.