A police spokesman in the town of Mito told Reuters that the fire broke out on the first floor of a maintenance facility that is about 50 metres from the experimental reactor, which is currently undergoing maintenance.The spokesman said the fire broke out around 8:40 p.m. (1140 GMT) and was under control about two hours later.
There were no injuries and authorities ruled out the possibility of a radioactive leak, he said.
The Joyo facility is located in Ibaraki Prefecture, northeast of Tokyo.
The facility was the site of a controlling rod malfunction in the spring of 2000, forcing the reactor to shut down.
The facility is operated by the state-run Japan Nuclear Cycle Development Institute.
Japan is heavily reliant on nuclear power although there have been a number of accidents over the past decade that have undermined public support for the programmes.
In September 1999, one uranium plant worker was killed in a uncontrolled nuclear fission reaction at a reprocessing facility.
The accident, attributed to poor management controls over the reprocessing, was the worst ever in Japan.
Japan has 51 reactors supplying about one third of the country's electricity needs.
Another JNC reactor, the Monju prototype fast-breeder reactor, remains shut since a December 8, 1995, accident in which it suffered a massive sodium coolant leak.
State-run JNC was launched in October 1, 1998, taking control of the three core fields of research and development that were previously run by the Power Reactor and Nuclear Fuel Development Corp (PNC), which came under fire for mismanagement.