Hundreds of people fled their homes as floods unleashed by Super Typhoon Saola swept through mainly rural villages in the northeastern Philippines, rescue officials said Sunday.

Saola brushed past the northeast section of the main island of Luzon overnight Saturday, bringing its 185-kilometre-per-hour (115-mile-per-hour) central winds within 125 kilometres of Tuguegarao, a city of about 160,000 people.

"The winds were not too strong but the rains were heavy last night," Ruelie Rapsing, a rescue official in Cagayan province, told AFP by telephone from Tuguegarao.

The provincial government's press office released photos on its Facebook page of knee-deep floodwaters swamping homes in the municipality of Aparri.

A total of 388 people were evacuated due to flooding in four Cagayan towns, with waters in two other towns also rising, Rapsing said.

There were also widespread electricity cuts across the province of 1.2 million people due to downed power lines, but otherwise there were no casualties or signs of serious damage, he added.

Saola headed south off Luzon's east coast early Sunday, with the state weather service saying it would stay in coastal waters instead of making landfall.

Rescue officials in Isabela and Aurora, east coast provinces south of Cagayan, told AFP there were no immediate reports of damage or casualties there.

The weather service said the main threat was from heavy rain that could trigger flash floods or landslides.

Up to 200 millimetres (nearly eight inches) of rain was forecast to fall along Cagayan and Isabela's coasts during the day.

The Philippines is hit by an average of 20 major storms each year that kill hundreds of people and keep vast regions in perpetual poverty.