More than 40 Philippine police commandos were killed in an 11-hour firefight with Muslim rebels which erupted while they were chasing one of the region's most wanted militants, police say.
The clash - which broke out despite a peace pact with the main rebel group - was "the single largest loss of life in recent memory by our security forces", said interior minister Manuel Roxas on Monday.
A total of 43 commandos were killed Sunday in the remote town of Mamasapano, a known rebel stronghold, on Mindanao island in the south, the national police chief Leonardo Espina told a news conference.
Regional police spokeswoman Judith Ambong said separately the bodies of 49 policemen were recovered.
Eleven police were injured but there was no information on any Muslim rebel casualties.
Almost 400 police commandos swooped before dawn on the hideout of the Bangsamoro Islamic Freedom Fighters (BIFF), a splinter group which rejects the peace pact, in search of Zulkifli bin Hir.
Roxas said police claimed to have killed Zulkifli, a bombmaker for the Jemaah Islamiyah (JI) group which staged the 2002 Bali bombings and other deadly attacks.
He is among the United States' most wanted militants, with a $US5 million ($A6.36 million) bounty for his capture.
But as the commandos were leaving they encountered the Moro Islamic Liberation Front (MILF), sparking a "misencounter", he said.
The 10,000-strong MILF, the main Muslim rebel group in the south, signed a peace treaty with the government in March last year.
The BIFF, a breakaway faction of several hundred Muslim gunmen, was not part of the deal.
President Benigno Aquino ordered an investigation into the incident, a major test of the accord intended to end a 40-year insurgency that has claimed tens of thousands of lives.
The MILF said police did not coordinate the operation as required under the ceasefire accord.
"There will be an impact but we are hopeful and confident that this will not derail the peace talks," Roxas said.
He said Zulkifli was believed killed based on pictures from the encounter site, but his body had not been recovered or positively identified.
The Malaysian is the most prominent of the 10 to 12 foreign JI members believed hiding in the Philippines. He slipped into the southern region in 2003 and has since been training local militants, according to the military.
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