At least three people have died and three are missing after landslides and floods hit a region in southern Japan that was recently battered by major earthquakes, officials said Tuesday.

Rescuers are searching for three people in the southern prefecture of Kumamoto where nearly 2,000 residents evacuated their homes, including those who had fled to safety after two huge earthquakes in April.

The 6.2-magnitude and 7.0-magnitude tremors were followed by more than 1,700 aftershocks, which broke up the ground in many areas, officials said.

The tremors left 49 dead and caused widespread damage.

Torrential rain has triggered widespread landslides and flooding in the area overnight.

Local residents reported swollen rivers flooding streets and houses with knee-high water, while others said they heard roaring noises in areas hit by night-time landslides.

More rain was expected in coming days, the weather agency said. It has issued heavy rain and thunderstorm warnings for Kumamoto and surrounding areas on Kyushu island.

A 92-year-old man died after a landslide hit his house in Kamiamakusa city, a local disaster management official said on condition of anonymity.

A 79-year-old man drowned in a flooded ditch in the town of Kosa.

The local government said in a statement that a third person had died, but did not provide details.

According to media reports, the victim was a 66-year-old man whose house was hit by a landslide in Uto city.

Local media also widely reported that the body of an 86-year-old woman was pulled from her house which was hit by a landslide in Kumamoto city.

Another person who lived with her remained unaccounted for, public broadcaster NHK said.

Officials could not immediately confirm a fourth death but said three people were missing.

The central government, which is supporting post-quake rebuilding in Kumamoto, has strengthened its crisis management department.

"We will take thorough measures to deal with this," said Chief Cabinet Secretary Yoshihide Suga.