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

Typhoon Khanun was lashing the Amami island chain, south of Kyushu, where four days of torrential rain 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 northwest and expected to graze Kyushu island through Wednesday afternoon, the Japan Meteorological Agency said.

Tuesday brought a brief lull in the rainfall for most of the region, but forecasters warned of more rain to come in some parts, saying it could trigger further landslides and floods, as well as high waves and strong wind.

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.

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 City, which sits at the foot of a volcano, has seen more than 80 centimetres (31 inches) 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. Roads in Aso remained flooded and inaccessible.

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.

A 55-year-old man died in Toyama prefecture apparently from heat stroke, while 688 people were taken to hospital due to heat exhaustion, public broadcaster NHK said.

One person died and nearly 700 others were taken to hospital due to heat stroke on Monday.

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.