At least 12 remain missing after deadly Typhoon Hagibis, which left as many as 13,000 homes flooded in 13 prefectures.

Rescue workers in Japan continued to search for the missing on Wednesday as the death toll from one of the worst typhoons to hit the country in decades rose to 74, public broadcaster NHK said.

Many people were drowned in the flooding after scores of rivers burst their banks.

Public broadcaster NHK said 12 people remained missing and more than 220 were injured after Typhoon Hagibis swept through the country over the weekend.

As of Wednesday morning, more than 5,000 people are still in evacuation centres in 13 prefectures, almost a third of them in hard-hit Fukushima Prefecture, 269km (167 miles), north of the capital Tokyo.

Across the country, 13,000 homes were flooded during the height of the storm, while 1,100 were partly destroyed.

Throughout the eastern half of the main island of Honshu, 52 rivers flooded.

Weather officials in Japan were quoted as saying that many places that flooded received up to 40 percent of their annual rainfall in just two days.

On Wednesday, residents in Fukushima Prefecture, which suffered the highest number of casualties, were busy dumping water-damaged furniture and rubbish onto the streets.

Many elderly remained in evacuation centres, unable to clean up their homes.

In Date city, not far from the site of the nuclear disaster in 2011, farmer Masao Hirayama piled damp books in the street in front of his house, adding to a mound of rubbish from the neighbourhood.

He said the water had reached about two metres (6.6 feet) deep in his house, when he and his son were rescued by boat and taken to an evacuation centre.

His wife and grandchildren had stayed with relatives during the storm.

“I feel down,” Hirayama, 70, said, adding that the flood had swept away his greenhouses and farming equipment. “All that is left is the land.”

Japan has mobilised over 100,000 rescue workers to help in the clean up after Typhoon Hagibis [Carl Court/Getty Images].

Hirayama said he had rebuilt his house in 1989, raising the ground level following a flood in 1986. His family plans to live on the second floor until he can make repairs, which he reckons could take three months

Survivors in Fukushima described how water rose rapidly to chest-height in about an hour, making it hard to escape to higher ground.

“Nobody from city hall has come to check on us yet,” Yoshinagi Higuchi said on Tuesday, as he and his neighbours piled sodden tatami mats and other damaged furniture onto the street.

Meanwhile, an evacuation centre came under intense criticism after it turned away two homeless men seeking shelter from a typhoon.

Shinzo Abe, the Japanese prime minister, promised on Tuesday to take action after reports emerged of the two men being denied entry to the shelter in Taito ward in the capital, Tokyo.

A 64-year-old homeless man told Japan’s Asahi Shimbun newspaper that he arrived at the Taito evacuation centre on Saturday morning.

“The wind was strong and it was raining and I wanted them to let me in,” he said.

Officials asked him to write down his name and address.

When he said he had an address in the northern island of Hokkaido, he was refused entry because he was not a resident of the ward and ended up spending the night taking cover under the eaves of a building.

Abe earlier said the government would set aside 710 million yen ($6.5m) for disaster relief. He has also proposed using 500 billion yen ($4.6bn) in reserves for the long-term recovery effort.

“It’s important to make sure the storm-hit municipalities have enough funds to rebuild their communities,” he was quoted as saying by NHK.