A government official told AFP a special crisis cell had been created to respond to the disaster and would hold a meeting chaired by Prime Minister Shinzo Abe this morning.

Flooding in Japan.(Reuters)

Hiroshima:

The toll in record rains that have devastated parts of Japan rose today to at least 44, officials said, with authorities issuing new warnings as torrential downpours continued.

Local media put the toll at 50, with dozens more missing and the number of fatalities expected to rise further.

The official toll includes one person killed last week, when the typhoon system that brought the heavy rains first made landfall in Japan, but most of the deaths have been reported in the last few days.

The rain, which has been worst in western parts of the country, has completely blanketed some villages, forcing desperate residents to take shelter on their rooftops with flood water swirling below as they waited for rescue.

The torrential downpours have caused flash flooding and landslides, and prompted authorities to order the evacuation of two million people.

Hundreds have been injured and dozens of homes have been completely destroyed in the disastrous downpours.

"We are carrying out rescue operations around the clock," Yoshihide Fujitani, a disaster management official in Hiroshima prefecture, told AFP.

"We are also looking after evacuees and restoring lifeline infrastructure like water and gas," he added. "We are doing our best."

A government official told AFP a special crisis cell had been created to respond to the disaster and would hold a meeting chaired by Prime Minister Shinzo Abe this morning.

On Saturday, Abe warned at an emergency government meeting that "the situation is extremely serious" and ordered his government to "make an all-out effort" to rescue those affected.

Tens of thousands of rescue workers, police and military personnel have been mobilised to respond to the disaster, and the meteorological agency has issued its highest level warning for affected areas.