Philippine troops battled Muslim extremists on a remote southern island on Friday where a day earlier three of Southeast Asia's top terror suspects were killed in a US-backed air strike, the army said.

Soldiers who approached the bombed area on the outskirts of a small village on Jolo island after the raid faced dogged resistance from surviving militants, regional military spokesman Lieutenant Colonel Randolph Cabangbang said.

"There is intermittent fire, the area is not yet secured," Cabangbang told GMA television in a telephone interview.

The troops had moved into the scene of the strike in an effort to retrieve the bodies of the three senior militants who were killed, as well as to take on the others who survived Thursday's aerial assault.

The military said 15 members of the Al Qaeda-linked Abu Sayyaf and Jemaah Islamiyah (JI) organisations were killed in the air raid, which followed months of surveillance on the sparsely populated and isolated hinterland of Jolo.

Cabangbang gave no indication as to the scale of Friday's fighting, but military chiefs said on Thursday that about 30 militants were at the scene when the bombings began.

The military said it had targeted, and killed, Malaysian Zulkifli bin Abdul Hir, alias Marwan, one of the United States' most-wanted terror suspects with a $5 million bounty on his head from the US government.

Zulkifli was one of JI's top leaders and a bomb-making expert who had been hiding out in the southern Philippines since 2003, according to the US State Department.

Also reported killed was Singaporean Mohammad Ali, alias Muawiyah, another JI leader who had been hiding in the Philippines since the group killed 202 people in a series of bomb attacks on the Indonesian island of Bali in 2002.

The third senior militant reported killed was Filipino Abu Pula, also known as Doctor Abu or Umbra Jumdail, one of the core leaders of the Abu Sayyaf that is blamed for the worst terrorist attacks in the Philippines.

The military claimed the killings dealt a major blow to the capabilities of the two terror groups, particularly their ability to strike in the Philippines.

Philippine armed forces spokesman Colonel Arnufo Burgos said on Thursday that the US military provided intelligence that helped in the success on the bombing raid.

A rotating force of 600 US Special Forces has been stationed in the southern Philippines since 2002 to help train local troops in how to combat Islamic militants.

The US forces are only allowed to advise the Filipino soldiers and are banned from playing a combat role.