Four hungry chickens clawed at rubbish in a deserted street that smelt of corpses as military helicopters skimmed the rooftops firing rockets while the Philippines' most beautiful Muslim city burned.

Marawi, a lakeshore city of minarets that is the centre of culture for the mainly Catholic Philippines' Muslim minority, is nearly empty after gunmen wielding black flags of the Islamic State (IS) group went on a rampage last week.

Despite a relentless military campaign, an unknown number of gunmen remain held up in pockets of the city and holding hostages, while up to 2,000 residents are trapped.

"These guys know how to fight. It looks like they have had some training," Marawi city police chief Parson Asadil told AFP on Monday in grudging acknowledgement as he manned a checkpoint.

At least one of his men had been killed and five are missing, he said.

The official death toll is 19 civilians, 17 soldiers, three police and 65 militants.

It is almost certain to rise.

A police commando told reporters in Marawi he suspected the still off-limits public market was full of dead bodies.

"The area smells bad," said the commando, Hamid Balimbingan.

"We still can't penetrate the area and that's why we're using helicopter gunships on them (gunmen)."

Those trapped are in danger of being hit by rockets or getting caught in the crossfire of the battles, while a lack of electricity, water, food and medical care could be just as deadly, according to the International Committee of the Red Cross.

"It really is a terrible situation," ICRC's deputy head of the Philippine delegation, Martin Thalmann, told AFP in Marawi. His team has been in contact with the trapped people via phone.

"Sick people have already died because they couldn't get out. There are elderly in there."

The military campaign involves dangerous house-to-house combat with the gunmen using sniper fire to deadly effect from key structures and buildings.

Helicopters also fly regularly over the areas being held by the militants and fire rockets, even with civilians known to be in nearby buildings.

- An empty city -

At a key city crossing, where local police chief Asadil's unit took shelter from the sun on the side of buildings while manning a checkpoint on Monday, the streets were empty except for the four scrawny chickens.

Shops nearby were boarded up, with glass facades riddled with bullet holes. A truck with a smashed windshield and blown-out tyres blocked the road a block away.

Before the fighting, Marawi had a population of 200,000 people, more than 90 percent of whom were Muslim.

It is one of the few dominantly Islamic cities left in the southern Philippine region of Mindanao, which is regarded as the ancestral homeland for Muslims who arrived in the country well before Spanish colonisers introduced Christianity from the 16th century.

Since the fighting began neighbouring towns and cities have been swamped with fleeing Marawi residents, some having walked two days from mountain villages to skirt the fighting.

At multiple military and police checkpoints outside of the city there were long lines while security forces cross-checked residents' faces against the mug shots of known terror suspects printed on large posters.

Some residents had nothing but the clothes on their backs as they walked into crowded evacuation centres.

"We are angry at them," mother-of-six Sunay Macudin, 28, told AFP, referring to the militants as she and her children and her elderly grandmother sat on the floor of a gymnasium-turned-emergency shelter in nearby Pantar town.

"This would not have happened to us if the gunmen had not come to our village."

Another Muslim resident expressed bewilderment at the reported goals of the gunmen: imposing a brutal form of rule such as that seen by IS in Iraq and Syria, with anyone not sharing their ideology regarded as the enemy.

"They are supposed to be part of our tribe, they are supposed to be our kin, but even we don't understand what their cause is," the man said.

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