A powerful typhoon smashed into Japan on Wednesday and headed for the stricken Fukushima nuclear plant, where workers raced to protect buildings and reactors that are leaking radiation.

Japan Ground Self-Defense Force soldiers place sandbags to reinforce embankments on Shonai River as Typhoon Roke strikes Nagoya, central Japan. [Japan Ground Self-Defense Force]

The storm, which was packing winds of up to 198 kilometers an hour, has killed at least five people, and a million were initially warned to leave their homes over fears torrential rains could cause widespread flooding.

At around 7 pm Typhoon Roke was centered 63 km northwest of Tokyo, heading northeast - toward the area that was devastated by a record earthquake and tsunami on March 11 that sparked nuclear meltdowns at Fukushima.

Hundreds of flights were canceled, ferry and rail services were suspended and roads closed as the country prepared for the full impact of the storm.

Roke comes less than a month after another vicious typhoon barreled through Japan, killing around 100 people in one of the deadliest storms the country has seen in decades and heaping more misery on the disaster-weary nation.

"We have taken every possible measure against the typhoon," said Naoki Tsunoda, a spokesman for Tokyo Electric Power Co, the operator of the crippled Fukushima Daiichi nuclear plant on the northeast coast.

"We have tied down cables and hoses while fixing equipment so that radioactive materials will not spread (in violent winds)," he said, adding operations on the ground and at sea had been suspended.

He said workers had also put tarpaulin over spots in buildings where rain could enter.

Around 20,000 people are thought to have died along the coast when the March tsunami rolled in, wreaking billions of dollars of damage.

The nuclear plant was sent into meltdown after its cooling systems were swamped by the waves, sending radiation into the air, sea and food chain in the world's worst atomic disaster since Chernobyl.

Five people have so far been found dead in central and western Japan in the latest calamity, NHK reported, while four people are missing, including a boy who disappeared on his way home from primary school.

The broadcaster said 55 people had been injured as torrential rain battered some areas and caused flooding in others.

Prefectures across eastern Japan issued landslide warnings, telling people to stay away from areas at risk.

A tornado warning was temporarily raised across the Tokyo area, but expired a few hours after it was issued.

Many of the initial evacuation advisories were dropped by lunchtime on Wednesday, but remained in effect for around 330,000 people nationwide.

Auto giant Toyota temporarily shut 11 of its 15 Japanese plants, which lie in the path of the storm.

"The second (afternoon) shift is stopped. (It is) not resuming today," company spokesman Dion Corbert said.

He said production was expected to resume on Thursday.

Mitsubishi Heavy Industries temporarily closed five of its aviation and engine plants in central Japan due to the storm, a company spokesman said.