Tolentino said an investigation was under way to determine whether the crash was caused by ground fire or mechanical trouble.
"The Muslims of the Philippines want autonomy and equal rights - democracy has failed them so they have taken up arms"
Shafiq, Dhaka, Bangladesh
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A military spokesman said he was trying to confirm reports that up to 30 members of Abu Sayyaf had been killed or wounded in the battle that was carried out with the co-ordination of the Moro Islamic Liberation Front (MILF).
"The enemy suffered a lot of casualties. We are still trying to get the exact number but their casualties are heavy," Major Eugene Batara, regional military spokesman said.
Lieutenant-Colonel Bartolome Bacarro said two members of Abu Sayyaf were dead and one of the dead had been involved in the beheadings of 10 marines on Basilan on July 10.
"The armed forces will press the fight," he said.
Manila blames the Abu Sayyaf - which wants a separate Muslim state in the southern islands of the Philippines - and renegade members of the MILF for the beheadings.
The MILF has admitted ambushing a number of marines in July after they entered their territory unannounced but denied being involved in the beheading.
This was the first military offensive on Basilan since the beheadings despite Gloria Macapagal Arroyo, the president, deploying thousands of troops to the region.
The largely Catholic central government has not launched an all-out attack saying it could pull the MILF, with which it wants to negotiate an end to 30 years of conflict, into the fighting.
Talks between the MILF, which signed a ceasefire with Manila three years ago, have not proceeded for nearly 12 months but are set to resume next week in Malaysia.
The government has vowed to destroy the Abu Sayyaf, which is known for beheadings, kidnappings and the bombing of a ferry in Manila in 2004 that killed more than 100 people.