The Philippine military insisted Monday it remained loyal to President Benigno Aquino, responding coup rumors that have swirled since a bungled security operation left 44 police commandos dead.

Aquino is facing the biggest crisis of his nearly five years in office over last month's assault in which the special forces killed a top Islamic militant but also unexpectedly came under heavy fire from Muslim rebels.

Two members of an Al-Qaida-linked group were killed in clashes with troops in the southern Philippines on Sunday, a military spokeswoman said.

Three soldiers and two militants were wounded in the fighting that erupted before dawn in the jungles of Basilan island, Captain Rowena Muyuela told AFP.

Eight members of an Al-Qaeda-linked group of Philippine militants have been killed in clashes with security forces in the country's south, the military said Saturday.

Thirteen members of a counter-terrorism task force were also wounded in the fighting with the Abu Sayyaf group on the remote island of Jolo on Friday, said the government unit's spokesman Ensign Chester Ramos.

Philippine President Benigno Aquino Friday demanded Muslim rebels surrender a top terror suspect who escaped a bloody police raid or be "run over" in a government manhunt.

In a televised address, Aquino sought to calm public outrage over the death of 44 police commandos in a chaotic bloodbath that targeted two most-wanted terrorists.

The Philippines accused China on Thursday of ramming Filipino fishing boats off a disputed shoal in the South China Sea, and demanded its powerful neighbour respect its sovereignty over the potential flashpoint territory. 

The foreign ministry said it has sent two notes of protest over the January 29 incident off Scarborough Shoal as well as the removal of critically endangered giant clams by Chinese fishermen in the area a week earlier.

The FBI has said that DNA analysis indicates one of the world's most wanted terrorists, Bali bomber Zulkifli bin Hir, was likely killed in a Philippine police raid last month that also claimed the lives of 44 officers.

Zulkifli, also known as Marwan, was the main target of the chaotic January 25 anti-terror operation on a remote town.

Muslim rebels who signed a ceasefire with the Philippine government must cooperate with an investigation into the killing of 44 policemen by some of their fighters, a presidential official said Monday.

President Benigno Aquino's spokesman Edwin Lacierda hinted that this might even involve calling on the Moro Islamic Liberation Front (MILF) to turn over some members to face criminal charges.

An eight-year-old girl and three men -- one with his hands bound -- were among those killed in a botched anti-terror police operation in the Philippines last weekend, a local official said Saturday.

Mamasapano town mayor Benzar Ampatuan said residents had told him police tied up the man to stop him tipping off their targets ahead of the pre-dawn raid, in which 44 commandos died in one of the force's bloodiest days in recent years.

Philippine government and Muslim rebel negotiators issued a joint plea Saturday for the country to stick to a historic peace accord that is now in peril after a deadly clash spurred calls for retribution against the guerrillas.

Both sides told a press briefing in Kuala Lumpur that two days of talks in Malaysia on disarming the rebels had made progress, and they vowed not to waver in implementing an accord on the voluntary surrender of weapons.

Philippine President Benigno Aquino pledged justice for the families of 44 police commandos killed by Muslim rebels during a botched anti-terror operation, as he led tributes on Friday -- a national day of mourning.

The men were killed in confrontations with two rebel groups in the southern Philippines on Sunday while on a mission to catch or kill Malaysian bomb-maker Zulkifli bin Hir alias Marwan, who is accused of involvement in the 2002 Bali bombings in Indonesia in which 202 people died.