A man drowned in a raging river while more than half a million people were advised to evacuate over the weekend as heavy rain lashed western Japan, officials said Monday.

The torrential downpours from Typhoon Nakri also led to the drowning of around 10,000 chickens after a river flowed over its banks near a poultry farm on Saturday, media said.

As the storm headed away from Japan, downpours continued in parts of the country on Monday with rainfall of up to 117 centimetres (46 inches) over the past three days, the national weather agency said.

"Very heavy rain is expected to fall in western Japan, mainly on the island of Shikoku, until Tuesday noon," the Japan Meteorological Agency said.

Shikoku is next to the southernmost main island of Kyushu.

The Fire and Disaster Management Agency said early Monday that about 550,000 people had been advised to seek shelter at public facilities since Saturday.

On Shikoku island, the body of a 40-year-old construction worker was found early Monday after he was washed away in a swelling river the previous day, police said.

Meanwhile a new super typhoon was building in the Pacific off the Philippines and was expected to reach Japan's southern Okinawa island chain on Thursday, the weather agency said.

The "very strong" typhoon, named Halong, was packing winds of up to 234 kilometres (145 miles) per hour as it slowly moved northwest at about 10 kilometres per hour, it added.

Last month typhoon Neoguri killed several people and left a trail of destruction in Japan's south.