At least 43 Filipino police commanders were killed in a clash with Muslim rebel forces after police carried out a raid in search of one of Southeast Asia's most-wanted terrorists, officials told the Associated Press.

Commanders from Philippine National Police's Special Action Force unit carried out the Sunday raid in a remote Maguindanao province village after receiving a tip that accused Malaysian terrorist Zulkifli bin Hir was hiding there.

But the botched raid, which police conducted without notifying the government or military, resulted in clashes between Muslim guerillas in the area, mainly from the Moro Islamic Liberation Front, national police Deputy Director General Leonardo Espina told the AP.

"There is sadness and bitterness because there are more than 40 bodies here," Interior Secretary Mar Roxas said of the raid carried out in the village of Tukanalipao.

Hir, one of the FBI's most-wanted terrorists, was likely killed in the raid, according to The Wall Street Journal.

Officials said the Special Action Force's biggest mistake was not telling MILF leaders they were carrying out operations in the area, which violated terms of a cease-fire reached between the government and Muslim rebels last March.

"They made a serious mistake," Mohager Iqbal, who negotiated for MILF during peace talks with the governmenet, said according to the WSJ.  "Instead of solving one problem, they have created many new ones."

PNP General Leonardo Espina, however, said police made "a judgment call" by not alerting the military or MILF leaders in order to maintain the "element of surprise," the WSJ reported. An inquiry is to be launched into police conduct.

Muslims in the mostly Roman Catholic nation have long fought for the right to self-rule in the south, the AP reported. About 150,000 people have been killed over decades of fighting. The peace agreement was seen as a landmark move towards an end to the rebellion and a step towards an autonomous region.

But now, with the botched raid, plans for any Muslim autonomous region are hanging by a thread.

"The peace process has now been challenged," Rommel Banlaoi, executive director of the Philippine Institute for Peace, Violence and Terrorism Research, told the WSJ.

"Above all, this indicates that the situation in Mindanao is very complicated, and that the current peace process is unlikely to end the violence."