A powerful typhoon was heading northeast to Japan's main island of Honshu on Sunday after lashing parts of the country's southern islands with heavy rains and winds that caused flooding and some minor injuries.

Typhoon Tapah was passing near Nagasaki in southern Japan on Sunday afternoon after hitting other parts of southern Japan, including Okinawa, the two previous days.

Japan's Meteorological Agency said the storm was moving northeast at a speed of 30 kilometres per hour (19 mph), with maximum winds of 162 kph (100 mph).

The agency warned of heavy rain, flooding and possible landslides through Monday in western Japan.

The typhoon hit Okinawa on Friday and Saturday and left 18 people with minor injuries. The storm disrupted air and train travel in the region during what is a three-day weekend.

In Nobeoka City in Miyazaki prefecture, a tornado believed to have been triggered by the typhoon damaged at least one house and injured two people slightly, according to the Fire and Disaster Management Agency.

The winds blew a cargo container into an electricity tower, causing power loss to some train stations in the area.

The city postponed Sunday's entrance exam for city employees due to the typhoon.

The approaching typhoon also caused fears in parts of Chiba, near Tokyo, which was hit hard by another typhoon earlier this month and is still recovering from the damage.

That typhoon damaged many houses and electric poles, causing widespread blackouts in the prefecture and triggering criticism and concern about ageing infrastructure systems in the country.

Cleanup and power restoration efforts continued Sunday in parts of Chiba.