Philippines army says it has killed three top militants from al-Qaeda.

AFP - The Philippine army said it killed three senior leaders from the Al-Qaeda linked Abu Sayyaf and Jemaah Islamiyah militant organisations in an air raid on a remote southern island on Thursday.

The three were among 15 militants killed on Jolo, a jungle-infested island where Abu Sayyaf members are suspected to be holding kidnapped foreigners, regional military commander Major General Noel Coballes told AFP by phone.

"Our troops on the ground have confirmed the death of 15 Abu Sayyaf and JI members, including Zulkifli bin Abdul Hir, alias Marwan, Mohammad Ali, alias Muawiyah, and Abu Sayyaf leader Abu Pula," Coballes said.

Zulkifli is a Malaysian leader of Jemaah Islamiyah, the militant organisation blamed for some of Southeast Asia's deadliest terrorist attacks including the 2002 Bali bombings in which more than 200 people were killed.

The US government has offered a $5 million reward for Zulkifli's capture.

Muawiyah, who goes by many aliases, is a Singaporean member of JI who fled to the Philippines shortly after the Bali bombings, according to a Philippine military intelligence officer.

Abu Pula, a Filipino, is a founder and one of the most senior figures of the Abu Sayyaf group, which was established in the southern Philippines in the 1990s with seed money from Osama bin Laden's Al Qaeda-network.

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 a spate of kidnappings in the remote and Muslim-populated south.

A rotating force of 600 US Special Forces has been stationed in the southern Philippines for a decade 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.

The Abu Sayyaf is well-known to have given refuge to Islamic militants from around the region such as JI leaders, who in turn have helped with training such as bomb-making skills.