The protesters braved pouring rain in Taipei to wave banners and placards reading "No nukes, no fear" and "Abolish nuclear power," amid tight security.
Police sealed off some streets in the area with barbed-wire barricades as organisers vowed to stage more protests if their demands were not met.
The plant outside Taipei has been one of the most contentious projects in Taiwan. Intense political wrangling has repeatedly delayed its construction, which began in 1999 and has already cost around USD 10 billion.
Lin has said that he was forced into taking the drastic move because the authorities ignored majority public opinion against the power station.
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"The matter is urgent as Mr Lin has been on hunger strike for five days," said protest organiser Liu Hui-min.
"We demand the government to stop building the plant immediately or we will continue the sit-in indefinitely."
Taiwan's President Ma Ying-jeou yesterday promised to let the public decide the fate of the facility in a referendum, but gave no timetable for the vote.
Like Japan, Taiwan is regularly hit by earthquakes. In September 1999 a 7.6-magnitude quake killed around 2,400 people in the deadliest natural disaster in recent history.