Thursday's ban was the first ban on rice shipments since the devastating nuclear crisis triggered by the March 11 earthquake and tsunami, The Japan Times reported.
Chief Cabinet Secretary Osamu Fujimura said the government instructed Fukushima Gov. Yuhei Sato to impose the ban. The prefecture also was instructed to conduct more tests on rice harvested in Onami.
The radioactive level was detected before the rice was shipped, Fujimura said.
The Fukushima prefecture government said Wednesday the cesium level was 630 becquerels per kilogram. The limit is 500 becquerels per kilogram.
Onami is about 50 miles from the crippled Fukushima No. 1 nuclear power plant. The contaminated rice was found when a farmer took unmilled rice to an agricultural cooperative for inspection Monday.
Prime Minister Yoshihiko Noda will keep on eating rice harvested in Fukushima prefecture at his official residence, the Times said. In his blog last month, Noda said he began eating rice from Fukushima Oct. 21.