It was not immediately clear whether civilians were among the dead. The violence has forced thousands of people to flee and raised fears of growing extremism.
On Friday, Duterte ordered his troops to crush the militants, warning that the country is at a grave risk of "contamination" by the Islamic State group. "You can say that ISIS is here already", he said.
Duterte has vowed to extinguish the threat of the fighters, whom he has said belong to the banned local Maute group but are being backed by criminals in the area.
He said this when met by reporters who had accompanied the PPM delegation to meet the Philippines Maritime Police representative, Maritime 1st Special Operations Unit commander Police Supt Cenen A Cuaresma. "If Allah wills it so, then we can not stop it", he said, pointing his finger in the air.
After receiving intelligence reports that Hapilon was hiding in Marawi city, security forces went to arrest him on Tuesday but were taken by surprise when they met massive resistance from Maute gunmen protecting him. He said he had spent the last few nights "praying that the bullets will not find their way to my house and hit us".
A military spokesman says troops are using helicopters to help clear militants from the besieged city of Marawi in the southern Philippines.
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The battle to clear the city of the gunmen was proving hard because they had scattered into small groups and were moving to different houses and setting up sniper positions, according to the military. "You do not have to be a Mindanaoan to make a stand on what is right, on what is just, and what is for the interest of the majority", said Reyes.
The National Council of Churches in the Philippines is equivocally against martial law in Mindanao, and is calling on the President to lift the declaration at the soonest possible time.
Solicitor General Jose Calida said Indonesians and Malaysians are fighting alongside the gunmen who attacked Marawi, a city of some 200,000 people on Mindanao island. But he said six foreign fighters are believed to have been killed in the Marawi fighting, including Malaysians, Indonesians and another nationality which he did not specify. "We suspect that but we're still validating", he said.
Malabang Police Chief Romeo Enriquez told The Associated on Friday that he is fine.
Hapilon, a leader of another Mindanao-based rebel group Abu Sayyaf, pledged allegiance to Islamic State past year and has formed an alliance with Maute. He also heads an alliance of at least 10 smaller militant groups, including the Maute, which have a heavy presence in Marawi and were instrumental in fighting off government forces in this week's battles.
Washington has offered a $5 million reward for information leading to Hapilon's capture.
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Bayan secretary general Renato Reyes Jr., meanwhile, reacted to Duterte supporters who mock non-Mindanao natives who oppose the martial law.
However, the imposition of martial law throughout Mindanao for at least 60 days could also affect the Philippine armed forces' handling of other armed conflicts on the island, including with the communist New People's Army (NPA) and various Moro insurgent groups.
He also said the bishops "balanced" their stance with the exhortation to "be obedient to the just commands of lawful authority, and not to provoke violent reaction" as he acknowledged their call to government "to remove the causes of terrorism, such as poverty and injustice, through just and accountable governance focused exclusively on the common good".
Duterte also warned that he may expand marital law nationwide.
In 1972, then-President Marcos imposed martial law and suspended habeas corpus throughout the Philippines, which facilitated widespread abuses by the military and other security forces, including detention without charge, torture, enforced disappearances, and extrajudicial killings.
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