A prominent Manila businessman paid $1 million in fines yesterday after pleading guilty to conspiracy in federal court in Alexandria for siphoning $3 million in kickbacks from Pentagon-financed contracts with the Philippine armed forces.

Raymond Moreno, 39, the businessman, also pleaded guilty to filing a false statement and to a tax violation in connection with the elaborate skimming operation that used inflated invoices from six American subcontractors to cover up the illegal payments, according to papers filed by the government.

John J. Ward, 66, an American employed by Moreno, also pleaded guilty to conspiracy in proceedings before U.S. District Judge Claude M. Hilton. Ward, who also resides in Manila, was given a suspended one-year prison sentence.

The pleas were the first to stem from a three-year-old investigation into fraud on $28 million in contracts Moreno obtained in 1983 with the Philippine armed forces. The contracts, financed by the Pentagon foreign military sales program, were part of an effort known as "Foresight Sierra" to modernize the Philippines' military communications system.

Moreno and Ward have agreed to cooperate with federal authorities who are investigating alleged wrongdoing by five of the six American subcontractors that dealt with Moreno and his three California-based firms, according to Theodore S. Greenberg, deputy chief of the Justice Department's fraud section.

The American firms named yesterday in court papers are Ocean Applied Research Inc.; Mitel Inc.; Trans World Communications Inc. and two subsidiaries of Harris Corp., Farinon and Digital Telecommunications Divisions. A sixth firm, Intercom Inc. of South Carolina, is defunct.

"Mr. Moreno would agree," Greenberg said during the hearing, "that the American contractors with whom he dealt . . . knew that the money they kicked back to Moreno's firms was money from the Defense Department's foreign military sales program."

A Trans World Communications spokesman said the firm had no comment on the allegations. Ocean Applied Research and Mitel could not be reached for comment. "We have no knowledge of any wrongdoing on the part of Harris or any of its operating units regarding any transactions with Mr. Moreno," a spokesman for Harris Corp. said.

According to court papers, Moreno required his American subcontractors to submit inflated invoices that included billing for "marketing services" they purportedly received from other Moreno-owned companies. In this manner, Moreno received about $3 million in kickbacks from Pentagon funds, the papers said. Moreno's tax violation stems from his failure to disclose this income on his U.S. tax returns.