Gen. Fabian Ver, former chief of staff of the Philippine Army, and Philippine businessman Eduardo M. Cojuangco appeared in Alexandria yesterday before a federal grand jury probing alleged fraud and kickbacks in Pentagon-financed military contracts to their country.

Ver and Cojuangco, who fled the Philippines and went to Hawaii with former president Ferdinand Marcos, were subpoenaed by the grand jury last week. Theirs were the first of what could be scores of U.S. courtroom appearances for Marcos associates as investigations progress into alleged corruption during his administration.

The Alexandria grand jury has been looking into possible kickbacks to Philippine officials for contracts totaling more than $100 million and partly financed under the Pentagon's foreign military sales and credits program, according to sources familiar with the probe. The jury began investigating in late 1984.

The contract that prompted the investigation is a $17 million deal for microwave communications to a California company called Amworld, set up in 1981 by Raymond Moreno, a close friend of Ver and Cojuangco, sources said.

Assistant U.S. Attorney Theodore S. Greenberg declined to say whether the two men are targets in the investigation. It is not known whether they answered questions by the grand jury.

Ver was in the grand jury room for about 15 minutes, exiting once to confer briefly with his lawyer, James E. Sharp. After his appearance, Ver, Sharp, Greenberg and investigators from the Defense Department's Criminal Investigative Service conferred for about 20 minutes in a side room.

Ver would not comment and left the courthouse. Sharp also refused to comment. "At this juncture, I'd just as soon not get into it," he said.

Ver, once Marcos' bodyguard and chauffeur, became a controversial figure when he was accused of conspiracy in the 1983 slaying of opposition leader Benigno Aquino. He was acquitted last December and then reinstated by Marcos as chief of staff.

Cojuangco, known as the "coconut king" of the Philippines, arrived at the federal courthouse ahead of Ver. He was with the grand jury for about half an hour, also conferring once with his lawyer. The lawyer declined to identify himself.

After shaking hands with prosecutor Greenberg, Cojuangco left the courthouse without comment.

Reputedly one of the Philippines' wealthiest entrepreneurs, Cojuangco owned the United Coconut Planters' Bank and ran a food and beverage processing empire. He maintained a private army to enforce his economic domination of the Philippine province of Tarlac.

The grand jury also had subpoenaed and received copies of documents brought to Hawaii with the Marcos party, U.S. government sources said.