Hundreds of Taiwanese students have occupied government headquarters to protest at a trade deal with China.
Police used water cannon and dragged out students one by one, clearing the building by dawn on Monday.
Close to 60 people were arrested and more than 100 hurt, reports said.
The protesters say the agreement with China would hurt Taiwan’s economy and leave it vulnerable to pressure from Beijing.
Another group of students and activists have occupied Taiwan’s parliament since early last week.
The students wants more scrutiny over all future dealings with China, including any trade agreements.
They also want the current deal – which would allow the two sides to invest more freely in each other’s services markets – to be scrapped.
The governing Kuomintang party says it is determined to ratify the deal with Beijing, which it says will boost the economy and create jobs.
China formally regards Taiwan as a part of its territory, despite the island governing itself for six decades.
The protests began early last week after ruling party’s lawmakers said a joint committee had completed its review of the pact, which was signed in June 2013 but has not yet been ratified by lawmakers.
Students broke into the legislature late on Tuesday and have since defied police efforts to evict them, using barricades made of furniture.
On Friday thousands of people rallied to support the students, and the opposition Democratic Progressive Party has also backed them.
On Sunday, President Ma Ying-jeou said that the occupation of parliament broke the law, adding: “I must say that [the pact] is completely for the sake of Taiwan’s economic future.”
Late on Sunday, some protesters pushed past riot police to storm the government headquarters, pulling down barbed wire and using ladders to access second-floor offices.
Violent clashes erupted as police moved to restore order.
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