Holding sunflowers and bright yellow banners reading "No Nuke", demonstrators rallied simultaneously in several cities across Taiwan, with the largest protest in the capital Taipei, said main organiser Tsui Shu-hsin.
"We demand the government halt the construction of the fourth nuclear plant and not to extend operation dates of the existing three," said Tsui, of the environmental group Green Citizens' Action Alliance.
Sunflowers symbolised a desire for clean and environmentally-friendly energy sources, organisers said.
Worries about Taiwan's atomic facilities grew after a 9.0-magnitude earthquake and ensuing tsunami struck Japan on March 11, crippling a nuclear power plant in Fukushima.
Organisers estimated a turnout of at least 5,000 in Taipei, but no police figure was immediately available.
Taiwan's government has said that in light of the Japanese catastrophe it would upgrade the earthquake-resistant designs of the three existing plants, which account for about 20 percent of the island's power supply.
Taiwan is regularly hit by earthquakes as the island lies near the junction of two tectonic plates.
In September 1999, a 7.6-magnitude tremor killed around 2,400 people in the deadliest natural disaster in the island's recent history.