Protesters chant anti-U.S. slogans during a rally in Manila demanding justice for the killing of 26-year-old Filipino Jennifer Laude. The U.S. military has the Marine accused of the crime, Pfc. Joseph Scott Pemberton, in custody aboard the USS Peleliu. (Erik De Castro/Reuters)

A U.S. Marine accused of strangling and drowning a transgender Filipino in a motel room toilet has triggered a public uproar in the Philippines, reviving sensitive memories of past incidents involving American service members and undermining the Pentagon’s drive to expand its military presence in the region.

Saturday’s killing of the 26-year-old Filipino, Jeffrey Laude, who dressed as a woman and used the name Jennifer, has emerged as a test of Washington’s push to send more troops to the Southeast Asian country for joint exercises and temporary deployments. It comes just six months after President Obama visited Manila to sign a deal to expand military cooperation with the Philippines.

The Philippine National Police have identified the suspect in the slaying as Pfc. Joseph Scott Pemberton, who was among 3,500 U.S. sailors and Marines visiting the Philippines for a joint exercise. Marine officials have not confirmed Pemberton’s identity but said they are holding the suspect aboard the USS Peleliu, an amphibious assault ship docked in Subic Bay.

According to Philippine authorities, Pemberton was on shore leave Saturday night in Olongapo City, about 50 miles northwest of Manila, when he befriended two Filipino women at a disco bar called Ambyanz.

Together, the three checked into a motel, the Celzone Lodge. Shortly before midnight, Laude asked the other woman, who went by the name Barbie, to leave “before the foreigner could discover that both were gays and transgender,” according to a statement issued Wednesday by the Philippine National Police.

Soon afterward, witnesses reported seeing the foreigner leave. A motel clerk inspected the room, thinking the occupants had left, and found Laude’s body slumped next to the toilet, according to police.

Police said the motel clerk and Barbie both later identified Pemberton from a photo lineup. Philippine authorities said prosecutors were preparing to file charges against Pemberton, a move that probably will set off a battle over whether he will be handed over to the Philippines to face justice or remain in U.S. military custody.

Pemberton, who is from New Bedford, Mass., enlisted in the Marine Corps last year and serves as an antitank missileman, according to the Marine Corps Times. He is a member of the 2nd Battalion, 9th Marines, based at Camp Lejeune in North Carolina.

Marine officials said they were fully cooperating with Philippine officials and noted that the Naval Criminal Investigative Service is working on the case alongside local police.

Chuck Little, a spokesman for Marine Corps Forces Pacific, based in Hawaii, said he could not confirm the suspect’s identity until charges are filed. He said that the NCIS was questioning other Marines as potential witnesses. Police in the Philippines said they have no other suspects.

In a reflection of the potential ramifications of the case, Adm. Samuel Locklear, the commander of U.S. forces in the Pacific, ordered that three Navy warships docked at Subic Bay for the exercises remain in port until the investigation is complete, Navy and Marine officials said. The annual exercise, known as Phiblex, or Philippines-U.S. Amphibious Landing Exercise, began Sept. 29 and ended Saturday.

“There’s a great sense of gravity over what happened,” said Rear Adm. John Kirby, the Pentagon press secretary.

Locklear was in the Philippines on Tuesday for previously scheduled talks with the chief of the Philippine armed forces, Gen. Gregorio Catapang. Afterward, Catapang said: “This will not affect our relationship with the United States.” But he added that the victim “is still a Filipino, and we have to fight for his rights and for justice.”

Under a long-standing agreement governing the rights of visiting U.S. service members, the Philippines has the primary right to exercise jurisdiction in such criminal investigations and can put U.S. suspects on trial. The U.S. military, however, can keep the defendant in its custody as the case unfolds.

The agreement includes a provision under which the Philippines could request that the U.S. military voluntarily hand over custody of a defendant. Some Philippine officials said they expect to make such a request in Laude’s death. Little, the Marine Corps Forces Pacific spokesman, and a U.S. Embassy spokeswoman in Manila declined to say how the United States might respond.

Laude’s slaying has ignited public protests and prompted some Philippine lawmakers to reassess the defense-cooperation accord that was signed in April. The Philippine government has said it will stand by the deal.

The murder investigation is drawing comparisons with a 2005 case in which another U.S. Marine, Lance Cpl. Daniel Smith, was accused of raping a Filipino woman in a van near Subic Bay while three other Marines watched and cheered.

Smith was convicted in a Philippine court and originally sentenced to life in prison. He was transferred to the custody of the U.S. Embassy in Manila and detained there until 2009, when his accuser recanted and his conviction was overturned. The outcome stirred suspicion among many Filipinos, in part because U.S. officials granted Smith’s accuser a visa to live in the United States after she changed her story.

The Philippines — once a U.S. colony — served as a keystone of the U.S. military presence in Asia for most of the 20th century.

In 1992, however, the Philippines rejected a proposed defense treaty and kicked the U.S military out of its sprawling naval base in Subic Bay. The United States was also forced to abandon nearby Clark Air Base after a volcanic eruption rendered it unusable.

In recent years, both countries have sought to rebuild defense ties largely because of the rise of China, which has clashed with the Philippines over disputed territory in the energy-rich South China Sea.