Hundreds of protesters who had been staging a demonstration against the trade pact pushed past riot police in full gear to storm the government headquarters, before the crowd was dispersed shortly after midnight.
Tensions exploded into the open on Tuesday when around 200 demonstrators, mostly young students, broke through security barriers and took over parliament's main chamber, the first such occupation of the building in the island's history.
President Ma Ying-jeou moved today to denounce the "illegal" occupation of parliament by students opposed to the trade agreement's ratification.
The network showed clashes between protesters and police holding shields, as well as an injured male protester lying on the ground being attended to by medical personnel.
The TV footage also showed blood streaming down the face of a male protester while citing hospital sources as saying more than 17 people were injured and more than 50 detained for questioning.
Student leader Lin Fei-fan called for calm: "I know many people were disappointed at what Ma said, but we have to maintain peace and non-violence principle."
"I must say that (the pact) is completely for the sake of Taiwan's economic future."
Ma warned of trade-reliant Taiwan being marginalised without the China agreement and similar pacts with other countries, as regional economic blocs emerge.
The agreement is designed to open up trade in services between China and Taiwan, which split 65 years ago after a civil war.
Opponents say it will damage Taiwan's economy and leave it vulnerable to political pressure from China, allegations rejected by Ma's ruling Kuomintang party.
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