The Philippines requested that medics aboard a Philippine navy ship near the village be allowed onshore to treat any of the Filipinos who may have been wounded Friday and take them and the others back to the country. There was no immediate response to the request.
Earlier Friday, Kiram told Philippine radio station DZBB that Malaysian police surrounding the village opened fire and that his group fought back.
"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.
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.
Associated Press writers Teresa Cerojano and Oliver Teves in Manila, Philippines, contributed to this report.