The Philippine military said Friday it had not been able to obtain proof that it killed three of Southeast Asia's most-wanted terror suspects, but insisted the trio had died in a US-backed airstrike.

Troops were sent to the isolated jungle area where Thursday's bombing took place on the remote southern island of Jolo, but they found no bodies, armed forces spokesman Lieutenant Colonel Arnulfo Burgos told reporters in Manila.

Burgos said the three senior leaders from the Al Qaeda-linked Abu Sayyaf and Jemaah Islamiyah (JI) networks, as well as 12 slain junior figures, had been taken away by fellow militants and quickly buried as per Muslim custom.

"After the airstrike, the bodies were taken immediately," Burgos said.

However he said the military was certain the top trio had been killed, based on intelligence "assets".

"Yes, its an A-1 (information). We have something but we cannot divulge all the other information because its an operational (secret)," he said.

The highest-profile militant reported slain was 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.

There was particular focus Friday on whether Philippine authorities could provide proof that the high-value trio had been slain because of previous incorrect claims of killing senior militants.

In 2009, the military said it had killed senior Abu Sayyaf commander Albader Parad but he gave a radio interview a few days later to prove he was still alive.

In 2001, then-president Gloria Arroyo said the Abu Sayyaf's top leader, Khadaffy Janjalani, had been killed. He later went on television to prove he was alive.

Burgos said Friday that security forces were confident of finding the bodies of the slain leaders, or at least pieces that would allow DNA confirmation.

But efforts to search the remote jungle area where the airstrike took place were hampered by gunfire from the surviving extremists, said regional military spokesman Lieutenant Colonel Randloph Cabangbang.

"There is occasional gunfire. They fire from a distance, just to disrupt our operations," he said.

The US military helped in Thursday's attack by providing intelligence support, military officials said.

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.

Spokespeople at the US embassy in Manila declined to comment on Thursday's attack, referring all questions to the Philippine military.