Local authorities say the Kuma River in the southwestern Japanese prefecture of Kumamoto is overflowing at seven locations along its length.
The officials issued flood information at 7:50 a.m. on Saturday. They urge residents to take immediate action to ensure their safety.
Authorities in parts of Kyushu, southwestern Japan, have issued evacuation orders following reports of landslides and flooding.
Several houses have been flooded in Ashikita and Tsunagi towns, Kumamoto Prefecture.
Japan's Meteorological Agency has issued a heavy rain emergency warning for parts of Kumamoto and Kagoshima Prefectures in the Kyushu region. The once-in-decades deluge is the highest warning level on a scale of 1 to 5.
Authorities are calling on people in the designated areas to evacuate or remain in safe areas. The warning has been issued for 16 municipalities in Kumamoto, and 4 in Kagoshima.
Officials in Tokyo are reporting 124 new cases on Friday. It's the highest daily tally since a national state of emergency was lifted in late May.
The number is sparking concerns that the capital may be on the verge of a second wave of infections.
Japan's industry minister says his ministry plans to study drawing up a roadmap to reduce coal-fired power generation, while aiming to accelerate a shift toward renewable energy.
Kajiyama Hiroshi was speaking to reporters on Friday about the ministry's drastic review of energy generation.
Japanese weather officials say heavy rain and thunderstorms will hit some parts of Japan's Pacific Coast through Saturday, raising the risk of mudslides.
The Meteorological Agency says warm and humid air has flown into the front and the low-pressure system, creating an unstable atmospheric condition mostly in western Japan.
Children in the western Japanese city of Kobe have thanked a giant panda with a hand-made present ahead of her return to China.
Tan Tan came to Kobe Oji Zoo 20 years ago to cheer up children affected by the 1995 Great Hanshin-Awaji Earthquake. She is set to go home after her lease expires on July 15.
The Tokyo metropolitan government says the number of new coronavirus cases has topped 100 for the second straight day -- sparking concerns that the capital may be on the precipice of another wave.
The number of virus cases has been steadily growing in Tokyo. One-hundred-seven were reported on Thursday and more than 120 on Friday -- the highest daily tally since a national state of emergency was lifted in late May and business activities began to resume.
Japan has asked the United States to extradite two Americans who are under arrest for allegedly helping former Nissan Motor chairman Carlos Ghosn to flee Japan while on bail.
US authorities arrested Michael Taylor and his son, Peter Taylor, in May for their alleged role in Ghosn's escape to Lebanon on a private jet.
The Tokyo Metropolitan Government says newly confirmed cases of the coronavirus topped 100 on Friday. The capital's daily total has hit triple digits for the second day in a row.
Japan's health ministry resumed its coronavirus contact-tracing app service on Friday.
The ministry said on Thursday that it fixed a glitch which was found just days after the smartphone application was rolled out on June 19.
Japan's ruling Liberal Democratic Party is moving to have a planned state visit by Chinese President Xi Jinping called off following the enactment of a national security law for Hong Kong.
Xi's visit has already been postponed due to the coronavirus pandemic.
Night sky watchers say what appeared to be a fireball was seen streaking over wide areas of Japan.
It was a phenomenon created by a fragment of a falling asteroid burning as it descends into the atmosphere.
Japanese weather officials forecast rain and thunder storms will hit wider parts of western Japan from Thursday night through Saturday.
The Meteorological Agency expects a seasonal rain front and a low-pressure system to approach the region on Friday and later.