At least 52 people have been killed while hundreds of thousands fled their homes as one of the strongest typhoons this year ripped through the central Philippines, authorities say.

Typhoon Kalmaegi has flooded large areas, including entire towns on the most populated central island of Cebu, where most fatalities occurred. Thirteen others are missing.

Videos show people sheltering on rooftops, while cars and shipping containers have been swept through the streets.

The official death toll excludes the six crew members of a military helicopter that crashed on Mindanao island, south of Cebu, after it was deployed to assist in relief efforts.

The aircraft went down on Tuesday near Agusan del Sur and was one of four sent to help.

"Communication with the helicopter was lost, which immediately prompted the launch of a search and rescue operation," the Philippine Air Force said. Later, a spokeswoman said six bodies had been recovered, believed to be of the pilot and crew.

The typhoon, locally named Tino, has weakened since making landfall early on Tuesday, but has continued to bring winds of more than 80mph (130km/h).

It is forecast to move across the Visayas islands region and out over the South China Sea by Wednesday.

"The situation in Cebu is really unprecedented," provincial governor Pamela Baricuatro said in a Facebook post.

"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."

Baricuatro declared a state of calamity in Cebu on Tuesday evening to facilitate disaster relief efforts.

Most of the deaths were due to drowning, reports said. The storm has been sending torrents of muddy water down hillsides and into towns and cities.

Damage to residential areas on Cebu was extensive, with many small buildings swept away and a thick carpet of mud left by the retreating floodwaters. Rescue teams took to boats to free people who were trapped inside their houses.

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

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

In total, almost 400,000 people were moved from the typhoon's path, Rafaelito Alejandro, deputy administrator at the Office of Civil Defence, told a news conference.

The Philippines is hit by an average of 20 storms and typhoons each year.

The latest comes barely a month after back-to-back typhoons killed over a dozen people and wrought damage to infrastructure and crops.

Super Typhoon Ragasa, known locally as Nando, struck in late September, followed swiftly by Typhoon Bualoi, known locally as Opong.

In the months before, an extraordinarily wet monsoon season caused widespread flooding, sparking anger and protests over unfinished and sub-standard flood control systems that have been blamed on corruption.

On 30 September, dozens were killed and injured after a powerful 6.9 magnitude earthquake struck the central Philippines, with Cebu bearing the brunt of the damage.

Typhoon Kalmaegi is forecast to move on to Vietnam, which is already seeing record-breaking rainfall.