The bodies of two women were found in a swollen river in Kagawa prefecture, some 550 kilometers (350 miles) west of Tokyo on Thursday, bringing the total number of the storm's victims since Tuesday to nine.
"We believe it is the body of a 72 year-old woman and her 45 year-old daughter ... who went missing after a flash flood hit the shelter where they were taking refuge," a local police spokesman said.
Three other people, aged between 74 and 84, were also found dead in Kagawa on Tuesday and Wednesday.
In the mountain village of Okawa in Kochi prefecture, about 170 people, including 134 schoolchildren, were rescued by helicopter from a lodge where they were attending an examination cram school.
They had been stranded there since Tuesday as heavy rain washed away all the roads to it.
"By 18:50 (0950 GMT), we rescued all of them," said a Kochi police official.
"One girl was taken to a hospital with suspected appendicitis. An elderly woman was also taken to a hospital to be treated for a leg injury," the spokesman said. "All the others were in good health."
In neighbouring Ehime prefecture, a 78 year-old man was found dead Wednesday after being swept into an irrigation ditch while on Tuesday a 74 year-old man was found dead in an overflowing irrigation channel.
Two more deaths were confirmed late Wednesday in Ehime.
The heavy rainfall caused by Typhoon Megi was expected to continue across wide areas of northern Honshu, Japan's main island, through Friday, the Meteorological Agency said.
The agency has warned of torrential rain, flooding and violent winds for areas along the Sea of Japan (East Sea), where the typhoon was located as of 6:00 pm (0900 GMT), heading northeast and packing 126 kilometer and hourmile per hour) winds.
The typhoon is expected to make landfall again in northern Japan early Friday.
Megi, which means fish in Korean, dumped 398 millimeters (16 inches) of rain in Shikokuchuo city in Ehime prefecture on Tuesday alone.
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