Prosecutor Prudencio Jalandoni filed charges of rape against the four Marines before a regional trial court in Olongapo, near the site of the alleged Nov. 1 rape, and sought their arrest and detention without bail.
The men, who were on liberty after participating with joint exercises with Filipino forces, are in U.S. Embassy custody.
In documents submitted to the court, Jalandoni alleged that Marine Lance Cpl. Daniel Smith raped a 22-year-old woman inside a van at Subic Bay free port, a former U.S. naval base northwest of Manila, while his fellow Marines cheered him on to the beat of loud music.
Also charged were Lance Cpl. Keith Silkwood, Lance Cpl. Dominic Duplantis and Staff Sgt. Chad Carpentier. Their hometowns were not immediately available.
Smith and the others, along with the woman, had been drinking at a bar and were rushing back to the USS Essex to beat a curfew, he said.
The Filipino driver of the van, Timoteo Soriano, who was initially considered as a key witness, was also charged as a "co-conspirator" for apparently doing nothing to stop the alleged rape.
The Americans have denied participating in or witnessing the incident. Some said in written statements that they saw Smith and the woman kissing and petting in the van's back seat but indicated there was no sign of struggle by the woman, according to Jalandoni.
Citing accounts of the Marines, witnesses and a medical examination of the woman, Jalandoni said he and other prosecutors concluded that Smith raped her while his companions egged him on.
"The complainant claimed that she was forced, although the answering respondents claimed that the sexual congress was consensual," Jalandoni said. "We believe that the victim was raped. She was screaming and struggling against Smith at the time.
Two other Marines, Corey Burris and Albert Lara, were cleared after submitting evidence that they were buying at pizza and were not in the van during the alleged rape, Jalandoni said. The U.S. Embassy said they were being released from its custody.
Those named in the charges could file a motion for reconsideration of the case within 10 days, Jalandoni said.
Another prosecutor, Raymond Viray, said the case would be a crucial test for the Visiting Forces Agreement, which allows American forces to conduct counterterrorism maneuvers with Filipino troops. Critics have expressed concerns that U.S. officials would use the accord to shield the Marines from prosecution.
U.S. Embassy officials have said they would cooperate with the Philippine government in the investigation, but have not indicated if they would agree to transfer the Marines to Philippine custody.
The embassy issued a statement saying it would continue to cooperate with Philippine authorities as the case moves to trial.
"The U.S. remains committed to seeing that justice is served, and looks forward to a fair and impartial process that can provide for a just outcome," the statement said.
The alleged rape has stirred emotions in the former American colony, and has been regarded by some as a black mark on U.S. counterterrorism training, which has been credited by Washington and Manila with helping Filipino troops crush many Muslim militants in the country's restive south.
The Marines had just taken part in a counterterrorism exercise in the northern Philippines and were on liberty at the time of the alleged incident.