Authorities have revealed that head of the victim was found inside a bag on Jolo island but his body is yet to be recovered.
Militants from the Abu Sayyaf group kidnapped the teacher near the Jolo town of Patikul on Oct 18 and demanded a two-million-peso (42,373-dollar) ransom.
Coming down heavily on this incident, President Gloria Arroyo's spokeswoman Lorelei Fajardo said in a statement, "We shall make them pay for the enormity of this savagery."
Abu Sayyaf group has been listed by the United States as a terrorist organisation. The group is believed to be behind many major attacks such as the 2005 firebombing of a ferry in Manila Bay which killed more than 100, and the abduction of American tourists in 2001.