The rally in the Shiba Park Sunday was attended by Nobel laureate Kenzaburo Oe, who urged the government to halt plans to restart nuclear power plants citing safety concerns.
The government has announced that it could allow idled nuclear plants to resume operation if their safety is confirmed by the new safety guidelines to be adopted in July.
Participants have so far collected over eight million signatures against the government's plans. A similar rally in Japan gathered some 170,000 participants in July last year.
Japan shut down all of its nuclear power generation facilities following the 2011 disaster at the Fukushima nuclear power plant. Of Japan's 50 reactors, only two have resumed operation so far.
In March 2011, Japan was hit by a massive 9.0-magnitude quake which caused a tsunami, claiming over 15,000 lives and triggering a number of explosions at the Fukushima plant.
The tsunami caused a partial meltdown at three of the plant's reactors. Radiation leaked into the atmosphere, soil and seawater, making the accident the world's worst nuclear disaster after Chernobyl in the then USSR in 1986.
Japan will need at least 40 years to recover fully from the nuclear catastrophe, scientists say.