M - almost 80 people are believed to be dead in Japan after three days of torrential rain made rivers burst their banks, Al Jazeera reported.
At one point, officials issued evacuation orders for almost 6 million people in 19 prefectures, Kyoda News reported.
Parts of western Japan hit by deadly floods and landslides are facing unprecedented danger as more downpours are expected, officials warn.
About 364 mm of rain fell in some two hours over the weekend in the city of Uwajima - approximately 1.5 times the average monthly rainfall for July, according to NHK.
The heaviest rainfall seen in Japan for decades has caused destruction over large parts of the country, particularly in the south-west, where 58 people are missing.
In the message, Francis expressed his solidarity with all those affected, offered his encouragement to rescue crews and said he was praying for the dead and injured "and the consolation of all those who grieve". About 40 helicopters were out on rescue missions.
The Pope also offered "encouragement to the civil authorities and all those involved in the search and rescue efforts as they assist the victims of this disaster" and upon all he invoked "abundant blessings".
The town of Kaita, on the outskirts of Hiroshima, was also heavily damaged by flooding and landslides.
Japan monitors weather conditions and issues warnings early, but its dense population means every bit of usable land is built on in the mostly mountainous nation, leaving it prone to disasters.
The rains crippled transportation networks, with bus and train services partly or completely shut down in 15 prefectures.
"There are many cases of disconnected water supply", he said, adding that officials were trying to provide relief so people would have access to drinking and bath water.
Landslide warnings were issued in more than a quarter of the nation's prefectures.
Some 73,000 troops of the Japan Self-Defence Forces, police and firefighters are still working on search and rescue operations, said government spokesperson Yoshihide Suga.
The Nuevo Leon state prosecutor's office reported in a statement that 12 people died in six bar attacks overnight in the municipalities of Monterrey, Guadalupe and Juarez.
At one building, drone footage showed the words "SOS" and "150 people!"
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