The death toll from Typhoon Kalmaegi in the Philippines climbed past 90 on Wednesday as the devastating impact on hard-hit Cebu province became clearer after the worst flooding in recent memory.

Floodwaters described as unprecedented had rushed through the province's towns and cities a day earlier, sweeping away cars, riverside shanties and even massive shipping containers.

On Wednesday, Cebu spokesman Rhon Ramos said 35 bodies had been recovered from flooded areas of Liloan, a town that is part of provincial capital Cebu City's metro area.

The grim news brought the toll for Cebu to 76. Earlier in the day, national civil defence deputy administrator Rafaelito Alejandro confirmed at least 17 deaths in other provinces.

"It was the major cities that got hit [with floods], highly urbanised areas," Alejandro said, adding that 26 people remained missing.

"The flood here yesterday was really severe," Reynaldo Vergara, 53, said, adding that everything in his small shop had been washed away.

"The river overflowed. That's where the water came from," he said.

"Around four or five in the morning, the water was so strong that you couldn't even step outside ... nothing like this has ever happened. The water was raging."

In the 24 hours before Kalmaegi's landfall, the area around Cebu City was deluged with 183 millimetres of rain, well over its 131-millimetre monthly average, weather specialist Charmagne Varilla said.

On Tuesday, provincial governor Pamela Baricuatro called the situation "unprecedented".

"We were expecting the winds to be the dangerous part, but... the water is what's truly putting our people at risk," she told reporters. "The floodwaters are just devastating."

In total, nearly 400,000 people were pre-emptively moved from the typhoon's path.

The Philippine military confirmed on Tuesday that a Super Huey helicopter, one of four deployed to assist typhoon relief efforts, had crashed on northern Mindanao island.

Hours later, air force spokeswoman Colonel Maria Christina Basco said the remains of six people had been recovered by troops.

As of 11am on Wednesday, Kalmaegi was moving westwards towards the tourist hotspots of Palawan, with winds of 130 kilometres per hour and gusts of 180kmh. (AFP)