MANILA >> Philippine police filed a murder complaint Wednesday against a U.S. Marine accused of killing a transgender Filipino, in an emotional case expected to test the country’s military ties with the United States.

Police Chief Inspector Gil Domingo said Marine Pfc. Joseph Scott Pemberton was the last person seen with the victim late Saturday, when they checked into a motel after meeting in a bar in Olongapo city northwest of Manila.

Jennifer Laude, whose former name was Jeffrey, was found with her head resting on the motel room’s toilet bowl, apparently after being drowned, Domingo said. The criminal complaint was filed with prosecutors, who will decide formal charges. There was no immediate comment from the U.S. Embassy.

A number of witnesses told investigators they saw Laude, 26, and Pemberton at the bar and at the motel, where the Marine was seen leaving shortly before the victim was found dead, Domingo said.

Police suspect Pemberton may have been angered when he discovered in the motel room that Laude was a transgender individual or because of an argument sparked by other reasons. Laude had not undergone gender reassignment surgery, Domingo said.

Pemberton took part in combat exercises involving thousands of American and Filipino troops. He is being held on the USS Peleliu in the Subic Bay free port, about 50 miles northwest of Manila, according to U.S. military officials.

U.S. Pacific commander Adm. Samuel Locklear, who was in Manila early this week for annual security talks with Philippine defense officials, initially ordered the Peleliu and other Navy ships to stay in the Philippines pending an investigation into the killing. All the ships except the Peleliu were later cleared to leave the country as the investigation progressed, according to Philippine officials.

“We will continue to cooperate fully with the Philippine law enforcement authorities in every aspect of the investigation,” State Department spokeswoman Jen Psaki said in Washington.

Dozens of activists burned a mock U.S. flag in a protest at the U.S. Embassy on Tuesday and tearfully demanded that Washington hand over Pemberton to Philippine authorities. They called for abolishment of the Visiting Forces Agreement, which allows U.S. forces to join large-scale combat exercises with Filipino troops and permits the U.S. to take custody of its soldiers who run afoul of Philippine laws.

The murder case emerged as security ties were blossoming between the United States and the Philippines. The longtime military allies signed a new accord in April that allows greater U.S. military access to Philippine military camps, and both countries have been vocal critics of China’s expansive territorial claims in the South China Sea.

“This is another test case of how strong and important this alliance is,” political analyst Renato de Castro said.

The U.S. and the Philippines disagreed over the custody of another Marine in an earlier criminal case.

The Marine was sentenced to life in prison on charges of raping a Filipino woman in 2005, but a Philippine appeals court overturned the conviction in 2009, allowing him to leave the country amid anti-U.S. protests.

___

Associated Press writer Matthew Pennington in Washington contributed to this report.