The protesters, who burst into the chamber late on Tuesday, say the agreement with China would hurt Taiwan’s economy and leave it vulnerable to pressure from Beijing.
The deal was signed in June 2013 but has not yet been ratified by lawmakers.
It would allow the two to invest more freely in each other’s services market.
The protesters moved in after ruling party lawmakers said a review of the pact by a joint committee was concluded.
“The trade pact must not be approved without careful deliberation and scrutiny in parliament,” a student leader was quoted by AFP news agency as saying.
The opposition had accused the government of going back on a pledge to review the agreement on a clause-by-clause basis.
Legislative Speaker Wang Jin-pyng on Wednesday called for “calm, reason and self-restraint” and said he hoped the confrontation would be resolved peacefully, Taiwan’s Central News Agency said.
China is Taiwan’s biggest trading partner and in recent years ties between the two have improved.
The two sides split at the end of the Chinese civil war in 1949, and China regards Taiwan as part of its territory.
Earlier this year, however, they held their first direct government-to-government talks. In the past, all talks have gone via quasi-official organizations.
They have also signed several trade and investment agreements in recent years – but some fear greater economic integration with China could threaten Taiwan.
Taiwan’s Central News Agency described the occupation of the legislature as “without precedent” and said that crowds had gathered outside the complex.
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