Members of the Philippine National Police Special Action Forces load bodies of police commandos into vehicles in Maguindanao on Jan. 26. More than 40 commandos were killed in a battle with Muslim guerrillas. (AP)

At least 43 Philippine police were killed in a clash with two Muslim rebel groups during a search for a Malaysian bomb expert on the FBI Most Wanted Terrorists list, threatening a peace pact with insurgents in the Mindanao region.

“This is the single largest loss of life in recent memory to our security forces,” Interior Minister Mar Roxas said at a televised news conference Monday in Cotabato City.

Police looking for Zulkifli Abdhir before dawn Sunday entered a town in Maguindanao province inhabited mostly by members of the Moro Islamic Liberation Front, Mohagher Iqbal, the group’s chief peace negotiator, said in a phone interview from Cotabato City on Monday. Some members of the Bangsamoro Islamic Freedom Fighters, a splinter group, also live there, he said.

“It’s an unfortunate event and it’s important that this doesn’t happen again,” Iqbal said, blaming the Special Action Force for failing to coordinate their operation with his group’s cease-fire committee. “We need to take care of the bigger issue, which is to bring peace to Mindanao.”

President Benigno Aquino III signed a peace pact with the 11,000-strong Moro Islamic Liberation Front in March to end a four-decade insurgency that has killed as many as 200,000 people and frustrated efforts to unlock investment in the mineral-rich south. The Sunday clash risks delaying a bill that will enforce the peace accord by setting up a new Muslim autonomous region with more powers and wealth.

“The event comes at a critical phase in the discussion of the Bangsamoro bill in Congress,” Julkipli Wadi, dean of the Institute of Islamic Studies at the University of the Philippines, said in a phone interview. “The parties can’t afford to let the situation deteriorate. They should pour water onto the fire by holding further discussions.”

In addition to the 43 officers killed in the firefight, 11 were wounded, national police officer-in-charge Leonardo Espina said at a televised briefing in Cotabato. Six members of the Freedom Fighters were killed in the encounter, Iqbal said. About five Moro Islamic men also died, Von Al Haq, a spokesman for the group, said by telephone Monday.

The government is trying to verify information that Zulkifli was killed during the operation, Defense Secretary Voltaire Gazmin told reporters in Manila on Monday. The U.S. Department of Justice indicted Zulkifli in 2007 on terrorism charges and offered a reward of as much as $5 million for information leading to his arrest or conviction.

Zulkifli is accused of having been a leader of the al-Qaeda-linked Jemaah Islamiah organization and suspected of being involved in a 2002 nightclub bombing on the resort island of Bali, Indonesia, that left 202 people dead. In 2012, the Philippine military said it had killed Zulkifli in an airstrike in Sulu province. Two years later, it said he was still alive, the Bangkok Post reported on Aug. 6, 2014.

“This incident and other recent acts of violence by other armed groups manifest the diverse security challenges that confound the peace process,” Miriam Coronel-Ferrer, who heads the government peace panel, said in an e-mailed statement Monday. Government resolve to finish legislation on the Bangsamoro basic law “is only further strengthened,” she said, adding that they seek to prevent further clashes with better cooperation.

Moro Islamic fighters acted in self-defense, Iqbal told reporters separately in a teleconference Monday, saying that more than one unit of policemen had staged the raid. He said a member of the Moro Islamic secretariat will travel to Manila to shed light on the Sunday firefight. The Moro Islamic and government peace panels will talk soon, he added.

Moro Islamic must explain why there were terrorists in their area of operations, Sen. Antonio Trillanes told ABS-CBN News in a live telecast Monday, adding that police should conduct an internal investigation. “We need to get the facts straight. We need to investigate both internally on the part of the police, and through the mechanisms of the peace agreement,” he said.

Bloomberg reporter Cecilia Yap contributed to this report.