MANILA, Philippines (AP) — At least three people were killed Friday as Malaysian police ended a three-week standoff with nearly 200 members of a Filipino clan who had occupied a village in eastern Malaysia, officials said.

Members of a Muslim royal clan from the southern Philippines landed in the coastal village of Lahad Datu in Sabah state on Feb. 9 to claim the territory as their own, citing ownership documents from the late 1800s. They ignored appeals from the Philippine president to leave immediately or face prosecution at home on charges of triggering an armed conflict.

Malaysian police officers move the bodies of two commandoes who were killed in a mortar attack after a exchange of fire between Malaysian security forces and the Sulu sultanate intruders in Tahduo, outside of Lahad Datu, Sabab, Malaysia on, Friday. Pic: AP.

Philippine Foreign Affairs spokesman Raul Hernandez quoted Malaysian Ambassador Mohamad Zamri Mohamad Kassim as saying police assaulted Lahad Datu on Friday and ended the standoff.

Philippine President Benigno Aquino III, who was traveling in northern Pampanga province, said, “It appears that what has been transpiring has ended.”

The village had been occupied by a group led by Agbimuddin Kiram, a brother of the head of a Filipino Muslim royal clan. The owner of the house where Kiram was staying was killed Friday, Hernandez said, without giving details. Kiram’s whereabouts were not known. Ten of the Filipinos surrendered to police, while the rest fled and were being pursued by Malaysian authorities.

Also in Friday’s assault, two Malaysian police commandos were killed and two others wounded in a mortar attack, the Malaysian national news agency, Bernama, reported.

The Philippines requested that medics aboard a Philippine navy ship near the village be allowed on shore to treat any of the Filipinos who may have been wounded and take them and the others back to the country, Hernandez said. There was no immediate response to the request.

Earlier Friday, Kiram told Philippine radio station DZBB in Manila that Malaysian police surrounding the village opened fire and that his group fought back. He said there were fatalities on the Filipino side, but there was no independent confirmation.

“They suddenly came in; we had to defend ourselves,” Kiram said. Sounds of shots were heard in the background while he was being interviewed by phone.

Hours later, Malaysian Home Minister Hishammuddin Hussein wrote on Twitter that the situation was “still under control completely.”

“I confirm that our security forces have not taken a single shot but were shot at at 10 a.m. this morning,” he wrote. He added that the Filipinos remained surrounded and that authorities had not fired any retaliatory shots.

On Tuesday, Aquino urged Kiram’s older brother in the southern Philippine province of Sulu, Sultan Jamalul Kiram III, to order his followers to return home and called their action a “foolhardy act” that was bound to fail.

The standoff elevated the Sabah territorial issue, which has been a thorn in Philippine-Malaysian relations for decades, to a Philippine national security concern. The crisis erupted at a crucial stage of peace negotiations — brokered by Malaysia — between the Philippine government and the Moro Islamic Liberation Front, the largest Muslim rebel group in the southern Philippines.

Aquino has said that the standoff may have been an attempt to undermine his government on the part of those opposing the peace deal, including politicians and warlords who fear being left out in any power sharing arrangements.