Two separate demonstrations took place in the capital city as engineers continued working to contain the crisis at the Fukushima Daiichi Nuclear Power Station.
Fukushima was seriously damaged by a massive earthquake and tsunami last month. Protesters said the incident was a wake-up call to the potential risk of another disaster.
"Now is the time to stop nuclear plants," Takashi Kamiyama told the Kyodo news service as he took part in a rally with is two young children. "I want to do what I can do for these kids."
Organizers said Japan's vulnerability to earthquakes made it likely that other nuclear plants could be seriously damaged in the future.