Philippine prosecutors have filed rape charges against four U.S. Marines, who allegedly attacked a Filipino woman while in the country to take part in a military exercise.

The six U.S. Marines originally accused, deny they raped a 22-year-old Filipino woman last month inside a rented van at the former U.S. naval base of Subic Bay, northwest of the capital Manila.

On Tuesday, the Olongapo City prosecutor's office filed rape charges against four of the Marines. The two others accused were cleared because of lack of evidence. The Filipino driver of the van was also charged as an accomplice.

The Marines were in the country as part of a two-week military exercise. Since the allegations emerged last month, the Marines have been in the custody of the U.S. Embassy in Manila - sparking an outcry from Philippine politicians, nationalists and women's groups, who want their immediate handover to the Philippine authorities.

Under a 1998 agreement governing visiting U.S. military forces in the Philippines, the Philippine government has jurisdiction over U.S. personnel committing offences in the country. But the U.S. military has the right to hold any personnel accused of crimes unless the Philippine government officially petitions the United States.

Prosecutor Prudencio Jalandoni, left, looks on as he files charges of rape against four US Marines before a regional trial court

Prudencio Jalandoni, chief prosecutor in the case, says all agencies of the Philippine government are working together to gain custody of the four Marines.

The U.S. government has said it will cooperate with Philippine officials on the case.

No trial date has been set yet for the case, which must be resolved within one year, according to the visiting forces agreement.

The United States operated several military bases in its former colony until 1991. After the September 11, 2001 terrorist attacks in the United States, the two allies have increased defense cooperation, including holding several joint military counter-terrorism exercises.