MANILA (Reuters) - The chief of the Philippines' elite police force has been recalled over his handling of an operation over the weekend to arrest two wanted Islamic militants that left over 40 members of the security force dead, the Interior Minister said on Tuesday.

Mr Manuel Roxas also said he had ordered an investigation into the operation that turned into a deadly 12-hour clash with Muslim rebels. The head of the Philippine National Police said the operation had not been cleared by top police officials.

Forty-four Special Action Force (SAF) officers were killed and 12 others wounded in the firefight in Mamasapano town, Maguindanao on Sunday. The police said eight Muslim rebels were also killed in the clash, which shattered a ceasefire that had held for three years.

"We have directed the administrative relief of SAF Director Leo Napenas from his current duties pending the outcome of this board of inquiry," Mr Roxas, the interior and local government secretary, told a news conference. "He has been recalled back to Manila. He was given a chance yesterday to help retrieve the bodies of his men. If there were lapses and someone is responsible for it, then he will be made accountable."

Mr Roxas on Monday described the incident as a "misencounter".

Nearly 400 SAF officers were involved in the operation aimed at arresting two militants who had taken refuge with fighters of the country's largest Muslim rebel group, Moro Islamic Liberation Front (MILF).

The two militants, Zulkifli bin Hir, a Malaysian member of the Al-Qaeda-linked Jemaah Islamiah militant group behind numerous bomb attacks in the Philippines, and Filipino Abdul Basit Usman, both carry a bounty on their heads.

Zulkifli, also known as Marwan, is the country's most wanted Islamist militant and the United States has offered a US$5 million (S$6.71 million) reward for him, while a US$1 million reward has been posted for Usman.

Officials said Marwan was likely killed in the firefight. "When the firefight ensued, according to them, Marwan was killed but they were unable to retrieve his body," Mr Roxas said, citing initial testimonies of police officers involved in the clash.

Pictures were taken of the alleged remains of Marwan, but the pictures will have to be verified, Mr Roxas added. He earlier said Usman escaped.

The MILF, which had been waging war for more than four decades in the south of the largely Christian country, have agreed under a peace accord to disband their force and surrender weapons in exchange for an autonomous government.