Armed stragglers supporting the Islamic State and hiding out among the ruins of a Philippine city after the end of a five-month battle still pose a threat to returning civilians, the military said Friday.

The admission came after authorities arrested an armed Indonesian militant this week and killed three other gunmen in the bombed-out southern city of Marawi.

"The main battle area, where most of the very heavy fighting occurred in the last few weeks prior to the liberation and the cessation of combat operation still harbors a number of stragglers," military spokesman Major-General Restituto Padilla said.

"These so-called stragglers continue to pose a huge threat to our people in Marawi as has been proven by the events of the past few days," Padilla told reporters in Manila.

• READ: IS-linked straggler killed in Marawi

Hundreds of local and foreign gunmen who had pledged allegiance to IS rampaged through Marawi, the principal Islamic city in the mainly Catholic Philippines, on May 23.

An ensuing US-backed military campaign claimed the lives of more than 1,100 people including around 900 militants, displaced 400,000 residents and reduced large parts of the city to rubble.

Padilla said the authorities were trying to confirm information provided by the captured suspect that more than 30 militants continue to hide out in building basements and tunnels.

Their hiding places were likely surrounded by booby traps and improvised explosive devices to prevent troops from approaching, he added.

The authorities were working "to ensure that not one of these terrorists may be able to escape because one terrorist who is able to escape has the potential of inflicting harm on many nationals -- on many of our nationals", he said.

More than 6,000 Marawi residents have been allowed to return home to areas that were previously cleared by authorities and did not suffer major damage, the authorities said Friday.

However the main battle area remained closed indefinitely.

Officials have said the fight for Marawi marked the Philippines' longest urban battle, with Defence Secretary Delfin Lorenzana estimating that the government will need $1.1 billion to rebuild the city.