The toll from the record rainfall has continued to rise, as rescue workers dig through the debris and find the remains of dozens of people reported missing.
Top government spokesman Yoshihide Suga said Friday that the toll was now 204 dead, with 28 people still missing.
Around 73,000 rescue workers including police and troops "are working as hard as they can, with the priority on saving lives", he said.
Abe, who earlier this week cancelled a foreign tour, travelled for a second time to areas hit by the disaster.
Television footage showed him visiting Seiyo in Ehime prefecture, where he visited homes damaged in the disaster and talked to residents trying to clean up.
On Friday morning, meeting with the government's taskforce on the disaster, Abe pledged new assistance.
The government has already said it will tap around $18 million in reserve funds from this year's budget, and Abe said $312 million in tax grants would be disbursed early to local governments in affected areas.
"I want local governments in disaster-hit areas to do all they can for emergency assistance and reconstruction, without hesitating to spend," he said.
The financial cost of the disaster is still being calculated, but the agriculture ministry said Friday it has assessed losses of at least $207 million.
That figure is likely to rise further as clean-up operations continue and the scale of the damage becomes clear.
It "could be the tip of the iceberg, as we are still unable to go and inspect fields," ministry official Yasuhisa Hamanaka told AFP.
Agriculture Minister Ken Saito said the cost of some vegetables had already shot up between 10-30 percent and that the ministry would be "closely monitoring" price hikes.
The size of the toll in what is now Japan's worst weather-related disaster in over three decades has prompted questions about whether authorities were properly prepared and acted effectively.
The English-language Japan Times daily noted that the flooding that engulfed one district of Kurashiki in Okayama prefecture was in line with forecasts from local authorities.
But "evacuation orders were issued by the city to residents in some areas of the district just minutes before the breach of the embankment took place," the newspaper said in an editorial.
"We need to scrutinise our defences against such disasters, identify the weak points and fix them."