Tropical Storm Khanun, which means jackfruit in Thai, was returning to the southernmost group of islands of Okinawa moving slowly northward, packing winds of up to 108km/h and hovering over Okinawa through Monday, according to the Japan Meteorological Agency.
Okinawa Governor Denny Tamaki warned residents to brace for torrential rains and mudslides.
"This could mean that the dangers about to hit the area where you are living are unusual and on a scale you have never experienced," he said of the storm.
He asked people to prepare escape routes to safety in advance.
"Do not let your guard down," he said.
Large parts of Okinawa, including the main city of Naha, were being slammed by extremely heavy rainfall, according to weather reports.
The storm hit the same area last week, killing two people, injuring dozens of others and squelching power temporarily to tens of thousands of homes, according to the Okinawa government.
Weather experts said the storm's wandering path was unusual and that it was moving slowly, affecting a wide area with strong winds and heavy rainfall.
It also appeared to be getting stronger, experts said.
The storm was expected to continue moving northward, possibly making landfall on Japan's southern major island of Kyushu by Wednesday or Thursday, the Japan Meteorological Agency said.
It comes a week after China's capital recorded its heaviest rainfall in at least 140 years over the past few days as remnants of Typhoon Doksuri deluged the region.
Landslides follow torrential rains in China
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