Hundreds fled their homes Sunday on a Japanese island already devastated by a typhoon for fear that torrential rain would trigger fresh mudslides.

The town of Oshima, 120 kilometres (75 miles) south of Tokyo, advised 2,300 residents in two districts on the island of the same name to evacuate, saying rain was expected to intensify due to a depression.

A total of 632 people had taken shelter in school gyms and community halls by early afternoon, an official at the town's administrative office said.

Many others were staying at relatives' homes in safer areas of the island, she said.

The meteorological agency has warned that rainfall could reach 40 millimetres (1.6 inches) per hour in the afternoon and has urged residents to be on alert.

The rain could trigger fresh landslides on the island where at least 27 residents were killed as a typhoon struck last week. Two others died in or near Tokyo.

Twenty-one people were still missing but search operations were suspended due to the bad weather.

Military airplanes flew 14 inpatients at the island's medical centre to hospitals in central Tokyo while Prime Minister Shinzo Abe cancelled his visit to the island set for Sunday.

Powerful typhoon Wipha triggered mudslides that buried some 30 houses and damaged more than 300 structures on Oshima last week.

Empress Michiko cancelled events scheduled Sunday at the imperial palace in Tokyo to celebrate her 79th birthday in the wake of the disaster.

An even stronger typhoon was churning north in the Pacific towards the Japanese archipelago.

Super Typhoon Francisco, currently packing winds of up to 198 kilometres (123 miles) per hour near its centre, is expected to be off the coast of Japan later in the week, according to the weather agency.