Hundreds of people gathered outside Taipei's Presidential Palace in the rain, many wearing yellow ribbons and stickers bearing the slogans "Say goodbye to nuclear" and "Nuclear go zero".
However, the crowd was noticeably smaller than the the thousands who joined last year's protest.
Organisers chalked up the demonstration's small showing to the Democratic Progressive Party's victory at the polls in January. The DPP has promised, along with a slew of new political parties set to enter parliament, to phase out the use of nuclear energy.
Tsai, who will take office in May, today reiterated her party's plan to make Taiwan nuclear-free within a decade.
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"To accomplish this goal, in addition to promoting energy efficiency we need to more importantly adjust the energy mix," the president-elect said in a Facebook post.
The DPP says it will put forward a raft of new energy policies once it takes office, including plans to increase the use of clean energy on the island.
The DPP has said it has no plans to restart the project.
The rally comes a day after Japan marked the fifth anniversary of a major nuclear disaster when the Fukushima energy plant was hit by a tsunami following an earthquake, knocking out power to its cooling systems and sending reactors into meltdown.
Taiwan, like Japan, is prone to frequent quakes as the island lies on a number of fault lines.
Protesters today also called on the government to propose new measures to safely store nuclear waste.
"If the waste can't be effectively processed, then we hope that the nuclear plants will be shut.