Philippine officials have removed the commander of a police special action force after at least 44 anti-terror commandos were killed in a clash with Muslim rebels.

The government's biggest single-day combat loss in recent memory shocked many and led to fears it could harm a recent peace deal with the biggest Muslim rebel group.

Interior Secretary Mar Roxas said Tuesday that police Director Getulio Napenas did not clear Sunday's assault on a top terror suspect with him or the national police chief.

Roxas said the commandos may have killed one of their terror targets, but also became entangled in separate firefights with hard-line Muslim insurgents and members of the main Muslim rebel group, the Moro Islamic Liberation Front. He said 44 commandos were killed and 12 others were wounded.