The raid pre-empted a plot by about 500 gunmen waving Islamic State group-style black flags to capture all of Marawi and kill as many Christians as they could, military officials say.
The Philippines and the U.S. government signed a Mutual Defense Treaty in 1951, where both countries committed to help each other in times of external armed attack. There was one from the Philippine National Police (PNP).
A security official who requested anonymity told the Manila Standard that IS-inspired extremists were planning terror attacks in Davao City, some areas of Maguindanao and Cotabato City, as well as the cities of Zamboanga, Lamitan and General Santos. He said they would discuss increasing security and signing an agreement to step up joint patrols.
"I did not realize that it was that bad because now it appears that Baghdadi himself, the leader of the ISIS, has specifically ordered terroristic activities here in the Philippines", Duterte said, without elaborating.
Defence Secretary Delfin Lorenzana, the designated administrator of martial law, has ordered the arrest of almost 200 militants, politicians and other suspected civilian backers of the unprecedented uprising in Marawi, the mosque-studded heartland of Islamic faith in the south of the predominantly Roman Catholic nation.
While the flag-raising was mainly to mark Independence Day, it also symbolized the reclaiming of city hall and other areas of Marawi by government forces.
Meanwhile, Justice Secretary Vitaliano N. Aguirre II has tapped the Department of Interior and Local Government (DILG) for manpower, food provision and other resources for the arrested Maute members and supporters detained at Camp Evangelista in the Mindanao city of Cagayan de Oro.
The Philippines has been fighting twin insurgencies from Maoist-led rebels and Muslim separatists in the south for almost 50 years.
Quoting military sources, local media reported that militants still control about 20 percent of Marawi city in Lanao del Sur.
The seizure of Marawi by fighters allied to Islamic State, including some from the Middle East, has alarmed South-East Asian nations which fear the ultra-radical group - on a backfoot in Iraq and Syria - is trying to set up a stronghold on Mindanao that could threaten their region.
Philippine President Rodrigo Duterte declared martial law on the island to help combat the militants.
The Filipino military has struggled to defeat the heavily-armed gunmen, who have used hostages and pre-existing bomb-proof tunnels to bolster their positions.
"You know the President has been working 24/7, meeting the troops, meeting the commanders, and then late last night, visiting the wounded", said foreign affairs secretary Alan Peter Cayetano.
Nevertheless, the Indonesian military chief urged everyone to be careful and on guard.
As the fight against ISIS-linked Maute militants continues in Marawi City, the Philippines this week appeared to reverse its position on global military cooperation.
China supports the Philippine government's "anti-terrorism" operations against Islamist militants, the Chinese foreign ministry said yesterday after United States special forces provided support to Filipino troops, reported AFP. The Philippine President will have talks with the Indonesian government to address the infiltration of ISIS that is reportedly coming from the some of the Islands off Borneo and in the Celebes sea.