Flood-battered southwestern Japan on Tuesday braced for a typhoon amid fears it could heap further misery on an area where at least 32 are dead or missing after record rainfall.

Typhoon Khanun was lashing the Amami island chain, south of Kyushu where four days of torrential rain have sparked landslides and flooding, forcing hundreds of thousands of people from their homes.

Khanun -- "jack fruit" in Thai -- packing winds of up to 126 kilometres (78 miles) per hour, was moving west-northwest at 30 kilometres per hour and was expected to graze the west of Kyushu island through Wednesday afternoon, the Japan Meteorological Agency said.

Tuesday brought a lull in the rainfall for most of the region as the weather agency said there was up to 9.2 centimetres (3.6 inches) of rain in the 24 hours to 4:20 pm (0720 GMT) in the north of Kyushu.

In hard-hit Minamiaso in Kumamoto prefecture, more than 670 people remained unable to return to their homes on Tuesday afternoon because of landslide fears.

"We started reconstruction work on damaged roads yesterday, but workers have been forced to step aside repeatedly by occasional rains," said local official Hideki Kuraoka.

"Even a small amount of rain could trigger mudslides and more downpours are expected this afternoon. We remain on high alert," he said.

Kuraoka said even though forecasters did not expect a direct hit from the typhoon, it was still a worry.

"We cannot know what damage will be caused by the typhoon," he said. "We are being extremely vigilant about it."

Most of the 400,000 people who were ordered or advised to leave their homes were allowed to return after authorities began lifting evacuation orders Sunday.

Roads in Aso city remained flooded and inaccessible.

Troops who were called in to help over the weekend on Tuesday continued their search for three people officially recorded as missing.

They recovered a man's body from a ditch in Aso on Tuesday, raising the total death toll from landslides and floods across the affected area to 29.

"The body belongs to a man, 55, who was one of the missing people," said a Kumamoto official.

Aso, which sits at the foot of a volcano, has seen more than 80 centimetres of rain over the last few days, triggering huge mudslides that swamped whole communities and killed at least 21 people in the city alone.

An AFP photographer who visited the city said some people who had been evacuated from their homes were seeking shelter in municipal buildings.

In scenes reminiscent of last year's devastating tsunami, families sat on mats on wooden floors, or gathered around televisions to watch the latest forecasts.

Other parts of Japan were dealing with soaring temperatures as the first really hot days of the sometimes punishing Japanese summer took hold.

The weather agency said temperatures of 39.2 degrees Celsius (102.6 Fahrenheit) were recorded in Tatebayashi, north of Tokyo, and 37.5 degrees Celsius in Hachioji, a city in western Tokyo.

On Monday, a man in his 80s died in central Niigata prefecture apparently from heat stroke, while nearly 700 people were taken to hospital due to heat exhaustion, local media said.

With the vast bulk of Japan's nuclear power stations offline in the aftermath of the tsunami-sparked Fukushima disaster, the country is being urged to cut down on electricity usage and the excessive use of air conditioners is being discouraged.