Philippine bishops have deplored the killing of at least 40 police officers who sought to arrest a rebel bombmaker believed to be hiding in the heart of a marshland in the country's restive southern region.

The Catholic Bishops' Conference of the Philippines (CBCP) denounced the gruesome manner in which members of an elite police commando unit were killed.

They had entered territory occupied by a group of separatist rebels who refuse to engage the government on a lasting peace accord when they were attacked on January 26.

Despite calls for retaliation, CBCP president Archbishop Socrates B. Villegas said the bishops are calling for sobriety as they urged negotiators to continue hammering out an agreement which will put an end to the violence in the south.

"While the CBCP vehemently condemns this act of violence against human life no matter what the avowed purpose of such violence may be, we cannot side with those who call for the discontinuance of peace talks," Villegas said in a statement.

"If anything, the sad incident underscores the necessity and the urgency of arriving at a solution that is not rushed but that is inclusive, principled and just to all," the bishop noted.

At least 43 bodies of members of the Philippine National Police's Special Action Force were recovered from the marshland.

The marshland was controlled by members of the Moro Islamic Liberation Front (MILF) and its breakaway faction the Bangsamoro Islamic Freedom Fighters (BIFF) at Mamasapano in Maguindanao province.

The MILF, the main Muslim rebel group in the south, signed a ceasefire agreement in March 2014 with the government. Both parties had agreed on the drafting of a law that gives the separatists autonomy in several areas of Mindanao.

The breakaway BIFF was not part of the deal.

The police officers sought to serve an arrest warrant to suspected Malaysian bombmaker and Jemaah Islamiyah member Zulkifli Bin Hir, also known as "Marwan," who was said to be hiding inside the MILF territory.

U.S. authorities placed a U.S. $5 million bounty on Marwan, who is believed to be behind several bomb attacks in Southeast Asia.

The MILF claimed the law enforcers did not coordinate their movements, resulting in the "misencounter."

Witnesses said some of the police officers were shot at close range, while others who sustained wounds in the 11-hour firefight had been "finished off."

"With profound sorrow but with faith in the Resurrection, the CBCP mourns with the families of the gallant policemen, victims of an utterly senseless act of violence in Mindanao, already weary from battle and conflict," Villegas said.