Six persons were arrested at the Philippine Embassy here yesterday during a protest demanding that the Philippine government identify the killers of opposition leader Benigno Aquino and explain the disappearance of a priest and other critics of President Ferdinand Marcos.

The protesters, timing the demonstration to mark the second anniversary of Aquino's assassination at Manila International Airport, also took the Reagan administration to task for what they called its "constructive engagement" with the Marcos government.

Though the term is one more commonly applied to U.S. relations with South Africa, the demonstrators argued that American military aid is supporting a dictatorship in the Philippines.

"Constructive engagement with the Marcos regime will never work," said Bill Christeson, who heads the Congress Education Project of the Friends of the Filipino People. Holding a white shirt, or barong, made to look as if it were bloodstained, he added, "Our tax dollars paid for this blood."

Aquino, the political archrival of Marcos, was killed Aug. 21, 1983, seconds after military guards escorted him off an airplane in Manila. Twenty-five military men and one civilian are on trial in connection with the slaying.

During yesterday's demonstration, three protesters entered the embassy, which had no guard in sight, at 10:30 a.m. and asked to present their demands directly to Ambassador Benjamin T. Romualdez or another top official. Three other demonstrators, carrying protest placards, stationed themselves in front of the embassy at 1617 Massachusetts Ave. NW.

After nearly an hour, members of the U.S. Secret Service moved in and arrested them. Those inside were charged with failure to quit the premises after embassy officials refused to meet with them. Those outside were charged with demonstrating within 500 feet of an embassy.

One of the demonstrators, Charito Planas, an exiled opposition leader who once ran on a platform with Aquino during a National Assembly election, called on embassy officials to explain the whereabouts of the Rev. Rudy Romano. According to Planas, Romano, a Catholic priest, was kidnaped by government troops more than a month ago.

"The kidnaping of Father Romano is merely the latest episode in the regime's attack on the Philippine clergy," said Planas, reading from a statement. "In the last five months alone, five priests and ministers have been shot and killed by Marcos security forces."

An embassy spokesman said the embassy would have no comment on the demonstration. He said the ambassador was in Manila.

In addition to Planas and Christeson, those arrested included Walden Bello, codirector of the Philippine Support Committee; the Rev. Douglas Cunningham of the Church Coalition for Human Rights in the Philippines; Kathleen Selvaggio, also of the Philippine Support Committee, and Dr. Roberto Castrence of the Philippine Medical Health Campaign.