Pope Francis expressed his "heartfelt solidarity" with all those affected by the worst flood disaster to strike western Japan in 35 years and said he is praying "especially for the repose of the deceased, the healing of those injured and the consolation of all those who grieve".
At least 64 people were killed and 44 missing, national broadcaster NHK said after the death toll had been put at 49 overnight.
Pope Francis is praying for the victims of Japan's flooding and is encouraging civil authorities involved in search and rescue operations.
At least 34,000 homes in western Japan were without power, and recovery work was hard because many roads were cut off by landslides. More than 100 people were confirmed dead in the disaster.
Since Thursday parts of western Japan have received three times the usual rainfall for the whole of July, setting off floods and landslides.
Millions of people were advised to evacuate their homes. Some 40 helicopters have been flying rescue missions.
Abe said earlier Monday that the government had dispatched 73,000 troops and emergency workers for the search and rescue effort.
Heavy rain was forecast to continue through Sunday in the west and the east, agency official Minako Sakurai told reporters.
Apart from this, around thousands of people have been displaced after their homes were destroyed in the natural calamity, reported the Japan Times.
"There are still many people missing and others in need of help".
Along with Hiroshima, other hard-hit regions where fatalities have been reported include Okayama, Ehime, Kyoto, Yamaguchi, Fukuoka, Kagoshima, Hyogo, Shiga, Gifu, Kochi and Saga prefectures.
According to Japan's Ministry of Land, Infrastructure, Transport and Tourism, the record rain had caused land disasters such as landslides at 201 locations in 28 of Japan's 47 prefectures.
The rains crippled transportation networks, with bus and train services partly or completely shut down in 15 prefectures.
Industry operations have also been hit, with Mazda Motor Corp saying it was forced to close its head office in Hiroshima on Monday.
The Japanese government set up an emergency headquarters, designed for crises such as major earthquakes.
An additional 13 people have since died from cardiac arrests, raising the total death toll to 103, according to Chief Cabinet Secretary Yoshihide Suga.