Chanting "Opposing the trade service agreement, safeguarding sovereignty", demonstrators attempted to push their way through a police cordon around parliament in Taipei.
Others tried to climb over the fence but were grabbed and pulled down by police. Two demonstrators were injured including a woman in her 70s, who fell and was hospitalised, the activist groups said.
"The pact will bring huge negative impacts on Taiwan's economy and lots of people will subsequently lose their jobs, but few people are aware of this," activist leader Tsai Ting-kui told AFP.
The pact is one of the follow-up agreements to the sweeping Economic Cooperation Framework Agreement signed in 2010 to reduce trade barriers between China and Taiwan.
Taiwan's China-friendly Kuomintang government said the pact would help lift the island's economy but the opposition Democratic Progressive Party (DPP) opposed it, saying it would hurt Taiwan's smaller service companies.
Lawmakers debated the agreement today but are not due to vote to ratify it until September.
Relations have warmed since Ma Ying-jeou of the Kuomintang party came to power in 2008 on a platform of beefing up trade and tourism links. He was re-elected in January 2012.
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