"I have told the governor of Fukushima prefecture to restrict shipments of rice harvested this year in the Onami district of Fukushima city," Chief Cabinet Secretary Osamu Fujimura said Friday.
According to Fujimura, the material was detected during pre-shipment tests and the contaminated rice had not been sold to consumers.
The sample reportedly came from a Fukushima city farm about 60 kilometers (37.5 miles) from the plant.
The Fukushima Daiichi nuclear plant was damaged by the earthquake and tsunami in March.
The damage resulted in radiation leaks and the worst nuclear crisis in Japan since the atomic bombing of Nagasaki and Hiroshima by the US at the end of WWII, which killed more than 200,000 people.
Japan's central government says 500 becquerels per kilogram of radioactive caesium is considered a safe limit, but the sample that led to Friday's ban contained 630 becquerels.
There have been a series of scares over radiation in food in Japan in recent months, including beef, mushrooms and green tea.