Samples of the rice measured caesium levels at 630 bequerels per kilogram while the government safety limit is 500 bequerels.
The government has ordered the Fukushima governor to restrict shipments of rice from Onami which will affect 154 farms that produced 192 tonnes of rice this year. The ban will not be lifted until the safety of rice in the area can be confirmed.
Bans on food products following the disaster on 11 March, when a massive earthquake and tsunami damaged the Fukushima nuclear power plant, are not new.
But rice has a special place in the Japanese diet and is eaten as much as three times a day in many homes.
On Thursday, the environmental group Greenpeace said it had detected radiation in fish sold at Japanese supermarkets although the levels remain within government safety levels.