A Maritime Self-Defence Force destroyer rescued 60-year-old Hiromitsu Shinkawa after discovering him floating on a piece of roof in waters off Fukushima Prefecture, two days after the disaster struck.

The man, from the city of Minamisoma which has been virtually obliterated, was swept out along with his house after the massive tsunami tore into Japan's northeast following a 8.9-magnitude earthquake on Friday.

He is conscious and in "good condition" after his rescue which took place around 12:40 pm (local time), ministry officials said, adding that he was transported to hospital by helicopter.

"I ran away after learning that the tsunami was coming," Shinkawa told rescuers according to Jiji Press.

"But I turned back to pick up something at home, when I was washed away. I was rescued while I was hanging to the roof from my house."

The government has said that at least 1,000 people are believed to have lost their lives in the disaster, and police estimate more than 215,000 people are huddled in emergency shelters.

However, the police chief of badly-hit Miyagi prefecture, which lies north of Fukushima, said that the death toll was certain to exceed 10,000 in his district alone.