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The Philippines said it killed three of Southeast Asia's top Islamic militants in a US-backed airstrike on Thursday, including a Malaysian bombmaker with a $5-million bounty on his head.

The Philippine army, aided by US advisers, launched a pre-dawn bombing raid on a remote southern island in which 15 members of the Al-Qaeda-linked Abu Sayyaf and Jemaah Islamiyah organisations died, military chiefs said.

"This is a big victory. There were three senior leaders (killed). This will have a very big impact on the capability of the terrorists," regional military commander Major General Noel Coballes told reporters in a teleconference.

Planes bombed the outskirts of a village on Jolo island where intelligence sources had informed the military that about 30 militant figures were based, Coballes said, adding no ground troops were initially deployed.

Among those the military said it killed was Zulkifli bin Abdul Hir, alias Marwan, a Malaysian who is accused of being a senior member of regional terror network Jemaah Islamiyah and behind multiple bomb attacks in the Philippines.

He is also accused of being the leader of Kumpulan Mujahidin Malaysia, a Malaysian group that like Jemaah Islamiyah wants to set up an Islamic state across Southeast Asia.

In 2007 the US government offered a $5-million reward for his capture, making him one of the United States' most-wanted men.

According to the US State Department's website that posts information about its most-wanted for terrorism, only four people have higher bounties for their capture, among them Al-Qaeda chief Ayman al-Zawahiri.

In Malaysia, authorities celebrated the reports of Zulkifli's death.

"We welcome the news of his demise as security forces in the region continue their fight against such militants," Ayob Khan Mydin Pitchay, head of Malaysia's special task force on counter-terrorism, told AFP.

The Philippine military said among the others to die in the air raid was Filipino Abu Pula, also known as Doctor Abu and Umbra Jumdail, one of the core leaders of the Abu Sayyaf militant organisation.

The Abu Sayyaf is blamed for the worst terrorist attacks in the Philippines including the bombing of a ferry in Manila that killed more than 100 people, as well as dozens of kidnappings in the remote, Muslim-populated south.

The third senior militant figure that the Philippine military said it killed was Singaporean Mohammad Ali, alias Muawiyah, another top name in Jemaah Islamiyah.

Jemaah Islamiyah is accused of carrying out many deadly attacks in Southeast Asia including the bombing of tourist spots on the Indonesian island of Bali in 2002 that killed 202 people, among them 88 Australians.

Muawiyah and Zulkifli were believed to have been hiding out on the Abu Sayyaf's bases on remote, jungle-infested southern Philippine islands since 2003, according to the Filipino military and the US State Department website.

Regional military commander Coballes said local soldiers and police who reached the site of the air raid after the attack confirmed that 15 militants were killed, including the three senior figures.

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 having a combat role, but they have claimed major successes over the past decade including helping in the deaths of many Abu Sayyaf leaders.

Philippine armed forces spokesman Colonel Arnufo Burgos told reporters in Manila that the US troops had again provided help in Thursday's bombing raid, which took place after months of monitoring and surveillance on Jolo island.

"The US has been providing us assistance in terms of training intelligence and they are helping us in the joint operation task force based in southern Mindanao," Burgos said.

"They provided us intelligence in this case."

A US embassy spokeswoman in Manila said she had no immediate comment.

AFP