Entire towns on the island of Cebu have been inundated, while cars, trucks and even massive shipping containers could be seen swept along by muddy floodwaters in videos verified by AFP.

In Cebu province alone, 39 people have been confirmed dead, provincial information officer Ainjeliz Orong told AFP, a figure she said did not include fatalities in provincial capital Cebu City, which are tallied separately.

At least five deaths have been recorded in other provinces, including an elderly resident who drowned in an upper floor of their home in Leyte province and a man struck by a falling tree in Bohol.

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

"The situation in Cebu is really unprecedented," provincial governor Pamela Baricuatro told reporters on Tuesday.

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

Local disaster official Ethel Minoza told AFP the bodies of two children had been recovered in Cebu City, where rescuers were still attempting to reach residents trapped by floodwaters.

Don del Rosario, 28, was among those in Cebu City who sought refuge on an upper floor as the storm raged.

"The water rose so fast," he said. "By 4:00 am, it was already uncontrollable -- people couldn't get out (of their houses)."

"I've been here for 28 years, and this is by far the worst we've experienced."

Scientists warn that storms are becoming more powerful due to human-driven climate change. Warmer oceans allow typhoons to strengthen rapidly, and a warmer atmosphere holds more moisture, meaning heavier rainfall.

Hundreds still living in tent cities after a 6.9-magnitude quake rocked the island in late September were "forcibly evacuated for their own safety", Cebu information officer Rhon Ramos told AFP by phone.

In total, nearly 400,000 people were pre-emptively moved from the typhoon's path, civil defence deputy administrator Rafaelito Alejandro said at a Tuesday news briefing.

- Military helicopter crash -

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

The Super Huey helicopter went down while en route to the coastal city of Butuan "in support of relief operations" related to the powerful storm, Eastern Mindanao Command said in a statement, adding search and recovery operations were underway.

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

"We're waiting to confirm the identities via forensics in order to ascertain their identities," she told reporters, saying two pilots and four crew members were on board.

The typhoon is now moving westwards through the Visayan island chain, weakening slightly with winds of 120 kilometres (75 miles) per hour and gusts of 165 kph.

The Philippines is hit by an average of 20 storms and typhoons each year, routinely striking disaster-prone areas where millions live in poverty.

With Kalmaegi, the archipelagic country has already reached that average, weather specialist Varilla told AFP, adding at least "three to five more" storms could be expected by December's end.

The Philippines was hit by two major storms in September, including Super Typhoon Ragasa, which tore the roofs off buildings on its way to killing 14 people in nearby Taiwan.