A total of 1.1 million people in Kagoshima and Miyazaki prefectures have been ordered to shelters, authorities say.

Authorities in Japan have issued evacuation orders for more than one million people in southern parts of the country hit by heavy rains, a year after deadly floods killed more than 200 people.

Small landslides were already being reported in parts of the affected area, public broadcaster NHK reported.

It said a total of 1.1 million people in Kagoshima and Miyazaki prefectures on the island of Kyushu had been ordered to shelters.

Landslides swept away several cars and buried a house in Kagoshima, the broadcaster said.

At least four people have been hurt, NHK reported later on its Twitter account, citing police and firefighters. In one case a car flipped onto its side in a mudslide, injuring a woman and her child, NHK said.

There were no official details on how many people had heeded the warnings to leave their homes.

At an evacuation centre in Kagoshima, elderly residents sat on the floor eating with their bedding and other belongings spread out around them.

The evacuation order is issued when a natural disaster is highly likely to occur and municipalities repeatedly urge residents to leave their homes, although the instruction is frequently ignored.

Residents take shelter in an evacuation centre in Kagoshima on Kyushu island on July 3, 2019 [Jiji Press/AFP]

It is the most serious warning issued before a disaster actually occurs. The scale’s highest level is activated once a disaster is declared and orders people to take measures to protect their lives.

About 868,000 people in Kagoshima, Kumamoto and Miyazaki prefectures are under a lower-level warning advising them to evacuate, according to NHK.

Sections of the Shinkansen bullet train on the southern island of Kyushu were disrupted by the heavy rain, which forced more than 150 schools to cancel classes, Kyodo news agency reported.

The Japan Meteorological Agency has warned that life-threatening landslides are possible at any time in parts of Kagoshima, adding heavy rain would continue overnight.

“If torrential downpours continue for hours in the same region, we might issue the special rain warning,” which is the highest-level warning indicating a disaster has occurred, agency official Ryuta Kurora told reporters.

“It will be too late to evacuate after the warning is issued,” he warned.

“Evacuate early without waiting for it,” he urged.

Kagoshima Governor Satoshi Mitazono said in a message to residents that the situation was “extremely dangerous”.

“A major disaster could happen anywhere, any time,” he said, adding that he had requested help from Japan’s Self-Defence Forces.

Japanese authorities are urging people to take shelter early after disastrous heavy rains last summer in the west of the country that killed more than 200 people.

Many of the deaths were blamed on the fact that evacuation orders were issued too late and some people failed to heed them. Entire neighbourhoods were buried beneath landslides or submerged in flood waters during the disasters.