At least four people died and some 7,000 travellers were left stranded at one of Tokyo's international airports after record rainfall flooded roads, rail lines and homes east of the Japanese capital.

Chiba, the prefecture bordering Tokyo, recorded over 360mm of rain in 24 hours in some parts during one of the busiest holiday weeks of the Japanese year.

Chiba city recorded 115mm in a single hour and Sakura 97mm, both records for both places.

The Japan Meteorological Agency issued its highest level of heavy rain warning for more than a dozen municipalities in the prefecture on Thursday but downgraded it on Friday as the rain eased, although it forecast more later in the day.

Takuya Hosomi, a forecaster at the agency, told a televised emergency news conference that unprecedented levels of rainfall had been recorded.

“This case was an extremely unusual situation, even by Japan's historical weather standards," Chiba’s governor, Toshihito Kumagai, told reporters on Friday.

"I have responded to many disasters in the past, but I have never experienced a case like this."

A man was found floating on a flooded road in Ichikawa and a woman in a submerged car in Sakura. Another person was pulled from a flooded car in Kashiwa and was presumed dead.

One person remains missing. Soldiers have been sent to the area to help with the disaster response.

More than 80 homes were flooded and nearly 230,000 residents across the prefecture were advised to leave for safety, according to Chiba officials.

About 23,000 households were still without power on Friday morning, down from 68,000 earlier, the TEPCO Power Grid said.

Around 7,000 people spent the night at the Narita international airport, queueing for blankets, water and snacks from staff before bedding down across the terminal, footage broadcast by NHK showed.

"We are never going to forget this trip," an American traveller stranded there with his family told the broadcaster.

The Ground Self Defence Force sent buses to collect some 4,000 people who had spent the night at the Soga station on the line serving the Tokyo Disney Resort, which reported no damage.

Hundreds more sheltered overnight at the Chiba prefectural government building, sleeping under foil blankets.

Some rail services connecting Narita to Tokyo had resumed by Friday morning, easing the congestion at the airport, though several lines remained suspended.

Major roads in Chiba were closed, including routes between Narita and central Tokyo, pushing drivers onto alternative routes, the highway operator NEXCO East said.

An airport spokesperson said all flights were scheduled to run normally on Friday.

Japan Airlines said some delays were possible but no cancellations were expected.

The flooding comes at the end of a fortnight of severe weather across Japan. A run of typhoons and extreme heat, which killed three lions at a Tokyo zoo and brought the first recorded “cruelly hot day”, have left the country reeling.

Scientists say a warmer atmosphere holds more moisture, making the heaviest downpours heavier.