At least 23 soldiers and police have been killed and 180 others wounded. Most of about 200 hostages have escaped or have been rescued, according to the military.
Two marines and a navy special forces member were killed in fierce clashes Thursday while three rebels died as troops, backed by helicopter gunships, attempted to clear a mangrove and the last few blocks of houses and buildings where rebel holdouts were believed to be hiding.
The more than 300 rebels involved in the standoff belong to a Moro National Liberation Front faction led by Nur Misuari. They signed a 1996 autonomy deal but refused to lay down their arms and later accused the government of reneging on a commitment to develop long-neglected communities.
They grew restive in recent months after peace talks between the government and a rival rebel group, the Moro Islamic Liberation Front, steadily progressed toward a potentially larger Muslim autonomy deal they felt would conflict with the 1996 pact they signed with the government.
Officials have filed complaints against Malik and other rebels for rebellion and for violating a Philippine law that upholds international humanitarian laws against the taking of civilian hostages and seizing communities.
Government prosecutors also plan to file criminal cases against Misuari, saying they have witnesses who could testify that he received updates by cellphone from Malik on the siege.
The rebels have been fighting for self-rule for minority Muslims in the south of the predominantly Roman Catholic nation since the 1970s.