The rice sample came from a Fukushima city farm about 50 km from the plant.
Japanese government is considering banning shipments from the area it was found.
There have been a series of scares over radiation in food in Japan in recent months – in beef, mushrooms and green tea among other products – but never before in the country’s staple, rice.
The rice was being prepared for market, but Chief Cabinet Secretary Osamu Fujimura said none had been sold.
The discovery highlights the difficulty of tracking the radiation which has been spread across eastern Japan by wind and rain.
Local governments in rural areas have set up testing centres to try to ensure contaminated products do not get into the food chain.
Last week the Tokyo Metropolitan Government also began testing samples bought at shops in the capital in an attempt to further reassure anxious members of the public.
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