Monju's relaunch was delayed for years in part because of outrage over the accident and the cover-up by the operator, which had initially released altered video footage of the fire in the facility.
The fire, which came only months after the plant had started generating electricity, was sparked after sodium coolant leaked from a pipe and reacted with oxygen and moisture.
No one was injured and no radioactivity released, but safety inspections later found more problems at the plant, including a corrosion hole in a ventilation duct that would have leaked radioactive emissions outside the facility.
"We demand that the government stop playing Russian roulette with our lives and permanently close down Monju"
Citizens' Nuclear Information Centre
"I never thought it would take so long to restart Monju," Hiromi Tanabe, Japan's atomic energy agency adviser, said.
"We know by now how important it is to disclose information to the public."
Japan, the world's second largest economy, has few energy resources of its own and relies on the nuclear power generated by more than 50 plants for nearly one-third of its domestic electricity needs.
Opponents of nuclear power stress the risk of earthquakes in Japan, which is located at the intersection of four tectonic plates, dotted with volcanos and is regularly hit by strong tremors.
The Tokyo-based group the Citizens' Nuclear Information Centre said: "We believe that Monju is an accident waiting to happen and that it is, therefore, irresponsible to restart the plant."
The group said the during the plant's long closure its equipment and piping had aged and that two active seismic faults below the site had now been recognised.
"We demand that the government stop playing Russian roulette with our lives and permanently close down Monju," the group said.
In July 2007, the world's biggest nuclear plant, Kashiwazaki-Kariwa, northwest of Tokyo, was shut down by a strong tremor, although no one was hurt. Only two out of its seven reactors have resumed operations.