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Torrential rain brought another deluge to southern Japan on Monday as the death toll from days of flooding and mudslides climbed to at least 49 people as rescuers searched for missing people.

Japan's Meteorological Agency issued the highest weather warning, a heavy rain emergency warning, for three prefectures in northern Kyushu after heavy rain hit the island's southern region over the weekend.

At least 49 people have been confirmed dead and 11 remain missing after three days of heavy rains spawned destruction over the weekend on the main island of Kyushu.

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More than 1.22 million people in the Kyushu region have been asked to evacuate, with residents asked to remain on high alert through Tuesday night.

People walk near piled-up debris from heavy rain in Hitoyoshi, Kumamoto prefecture, southern Japan Monday, July 6, 2020.

People walk near piled-up debris from heavy rain in Hitoyoshi, Kumamoto prefecture, southern Japan Monday, July 6, 2020. (Kyodo News via AP)

Some 1,500 people have taken shelter at 86 different evacuation centers across Kyushu as of Sunday afternoon.

"The water level of rivers suddenly rose in the Saturday rain. I am worried because I don't know how the rain is today," Shoko Matsunaga, 49, told Kyodo News.

Rescuers search for missing persons at the site of a landslide in Tsunagi town, Kumamoto prefecture, southern Japan Monday, July 6, 2020.

Rescuers search for missing persons at the site of a landslide in Tsunagi town, Kumamoto prefecture, southern Japan Monday, July 6, 2020. (Takuto Kaneko/Kyodo News via AP)

More heavy rain fell on Monday, with water seen flowing down a street in Hiroshima.

Army troops and other rescuers worked their way on Monday through mud and debris along the flooded Kuma River, where many houses and buildings were submerged nearly to their roofs.

A military helicopter could be seen evacuating stranded residents on Saturday, hovering over a house before winching a person to safety.

Japanese broadcaster NHK said some parts of Japan were experiencing levels of rainfall not seen in several decades.

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The riverside towns in Kumamoto city were among the most devastated, where 40 bodies were recovered.

A couple walks near debris from a heavy rain in Kumamura, Kumamoto prefecture, southern Japan Monday, July 6, 2020.

A couple walks near debris from a heavy rain in Kumamura, Kumamoto prefecture, southern Japan Monday, July 6, 2020. (Kyodo News via AP)

An evacuation in that area was not mandatory and many people are believed to have opted to stay at home because of concerns over catching the coronavirus, even though officials said shelters were adequately equipped with partitions and other safety measures.

The dead included 14 of the 65 elderly residents of the nursing home next to the Kuma River, which is known as the “raging river” because it is joined by another river just upstream and is prone to flooding.

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The river rose abruptly and its embankment gave in, causing floodwaters to gush into the nursing home, where most of the residents were bedridden or wheelchair users.

A woman is helped to get into a police vehicle to move from a shelter to another shelter in Kumamura, Kumamoto prefecture, southern Japan Monday, July 6, 2020.

A woman is helped to get into a police vehicle to move from a shelter to another shelter in Kumamura, Kumamoto prefecture, southern Japan Monday, July 6, 2020. (Kota Endo/Kyodo News via AP)

Japanese Prime Minister Shinzo Abe said the rain was forecast to head east by Wednesday, according to Reuters.

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“I urge all citizens to carefully follow the information provided by local authorities and stay alert to take actions to protect their own lives,” Abe said during a government meeting.

The Associated Press contributed to this report.