The torrential downpours have caused flash flooding and landslides across central and western parts of the country, prompting evacuation orders for over two million people.
"There are still many people whose safety has yet to be confirmed," he added.
Top government spokesman Yoshihide Suga said the death toll in days of record rains now stood at 48, but the toll is expected to rise further, with local media saying over 50 people were dead and dozens more missing.
The rain has completely blanketed some villages, forcing desperate residents to take shelter on their rooftops with flood water swirling below as they wait for rescue.
Over two million people have been told to evacuate, but the orders are not mandatory and many remained at home, becoming trapped by rapidly rising water or sudden landslides.
The meteorological agency issued its highest level alert for two new regions today, while lifting the alerts for other areas where rains were subsiding.
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