The number of people killed by a powerful storm that pummeled the central Philippines over Christmas has risen to 50, authorities have said.

The increased death toll makes Typhoon Phanfone the nation's deadliest storm of 2019.

Phanfone's destructive winds and heavy rains brought down homes and destroyed commercial buildings mainly in the central island of Visayas, affecting more than two million people.

At least 80,000 remain in emergency shelters and might have to stay until the New Year, given the scale of the destruction.

"We're sad that some of our countrymen are still in evacuation centres, but we assure them they will continue to receive support until they get back on their feet," national disaster agency spokesman Mark Timbal said.

Five people are still missing after the storm, which also left 143 injured.

The death toll - up from 41 on Sunday - included three sailors who died after their vessel capsized, a policeman electrocuted by a toppled post, and a man struck by a falling tree.

Typhoon Phanfone, locally called Ursula, was the 21st cyclone this year to hit the storm-prone Philippines.

Many of the storms wipe out harvests, homes and infrastructure, keeping millions of people in perpetual poverty.

Though much weaker, Phanfone tracked a similar path as Super Typhoon Haiyan - the country's deadliest storm on record which left more than 7,300 people dead or missing in 2013.