Demonstrators made use of a national holiday to hold the protest, one of the biggest anti-nuclear rallies since a tsunami and earthquake triggered a nuclear disaster at Japan's Fukushima nuclear plant last year.
Organizers said the number of participants was estimated to reach 170,000. Those taking part included Nobel-winning author Kenzaburo Oe and musician and composer Ryuichi Sakamoto.
The rally in and around Yoyogi park came a week after a nuclear reactor at the Oi plant in western Japan resumed full operations last week, the first plant to restart since Japan shut down its atomic stations in the wake of the Fukushima disaster in March 2011.
Protesters called for a complete end to nuclear power in Japan and demanded the resignation of Prime Minister Yoshihiko Noda, who ordered the restart.
In mid-June, Noda gave the green light for two reactors at the Oi plant to restart operations, citing the danger of possible power shortages this summer. The second reactor at Ohi is set to go online later this week.
A parliamentary report deemed the accident at the Fukushima plant to have been man-made, blaming it on a lack of cooperation between the plant operator, government and regulators. It is considered the biggest nuclear disaster since Chernobyl in 1986.
Before the disaster, Japan generated 30 percent of its energy from nuclear reactors. Opinion polls have shown that a large majority of Japanese now opposes nuclear power.
tj/ng (afp, AP)