A soldier also died, the military reported, bringing the death toll from 11 days of fierce street battles in the southern port city of Zamboanga to at least 114.
The fresh casualties came as an international human rights monitor issued a report alleging severe human rights abuses committed by both sides, including the rebels deliberately picking out Christians to use as human shields.
"Both sides need to do all they can to prevent further loss of civilian life," Human Rights Watch Asia director Brad Adams said.
Three military brigades, or about 4,500 soldiers, have been deployed to neutralise the rebels, according to national military spokesman Lieutenant-Colonel Ramon Zagala.
But the rebels have frustrated the military efforts and prevented a full-out assault by hiding in residential neighbourhoods and holding residents hostage. The military said the rebels may still be holding about 25 civilians.
Nevertheless, the military has pledged to kill or capture the rebels unless they surrender.
The military has given varying estimates of how many rebels are believed to still be holding out, from 30 to 70.
It has reported killing 94 rebels and detaining another 93.
Human Rights Watch detailed one incident on the third day of the conflict in which it alleged the military shot repeatedly at a group of rebels who were using Christian hostages as human shields.
"The shooting was relentless," it quoted one survivor, Monica Limen, as saying. It said Limen's 20-year-old son was killed in the crossfire.
Military spokesman Zagala denied soldiers had fired at hostages, or committed other abuses.
"If there are human shields we refuse to fire. If we had not been following this policy this fight would have been over a long time ago," he told AFP.
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