Abe told parliament on Tuesday the homeless men should have been given refuge,and he promised to take action to prevent similar cases in future.
One reason why the storm caused such severe impacts is that the inner core of the typhoon remained intact as it swept across Tokyo.
Nearly 8 million people were advised to evacuate during the deluge and 200,000 people were without power.
The Brave Blossoms were playing for more than a quarter-final berth on Sunday.
One woman fell to her death as she was being transferred to a rescue helicopter.
Tournament officials have announced the Pool A thriller will be played on Sunday night as scheduled.
The typhoon due to make landfall late on Saturday has already brought record-breaking rainfall as the weather bureau warns of floods and landslides.
The Wallabies had to draw on their reserves of resilience when worsening weather forced them to abandon a weekend trip to Tokyo.
For the four-decade-old disco band with the same name as Japanese typhoon,the sudden indirect publicity could"spark lots of concert offers".
The super storm is presenting a huge logistical and communications challenge for World Cup organisers,but the fallout could be only just beginning.
The Japan Meteorological Agency warned that the south-eastern Tokai region could be deluged by up to 78 centimetres of rain in a 24-hour period.