The central government told Fukushima Governor Yuhei Sato to "halt shipments of all cattle in Fukushima to meat-packing factories," chief government spokesman Yukio Edano told reporters.
Around 650 beef cattle are thought to have been contaminated with radioactive caesium in hay they had eaten before being sent to meat processing facilities across Japan since late March, with some of the meat consumed.
Beef from the cattle, which were mainly from Fukushima, was shipped to most of Japan's 47 prefectures.
The hay was apparently contaminated by the release of radioactive materials from the Fukushima Daiichi nuclear plant after it was hit by the March 11 earthquake and tsunami, which triggered reactor meltdowns at the facility.
In the latest food scare associated with the disaster, cows from farms outside the 20-kilometre (12-mile) Fukushima nuclear no-go zone were found to have eaten contaminated hay, triggering fears that radioactive fallout reached a wider area than thought.
On Monday, Fukushima officials told a news conference that they detected up to 157,000 becquerels of radioactive caesium per kilogram in straw used at the farms -- about 520 times the government-designated limit.
The government has sought to reassure the public that there is no immediate health threat from eating standard quantities of beef, even if it is tainted.
The accident at the Fukushima Daiichi plant was triggered when the March 11 earthquake and tsunami crippled cooling systems, sparking reactor meltdowns, explosions and the release of radiation into the air, sea and soil.
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