Clashes between Taiwanese police and protesters occupying two government buildings on Monday resulted in the arrests of dozens and more than 160 injured.
Water cannon was deployed outside the cabinet building against the protesters, mainly students, who briefly occupied the government's headquarters on Monday.
“The government will never tolerate the occupation of government buildings, which seriously hinder the operation of our government,” presidential spokeswoman Garfie Li said.
Activists were still inside the nearby parliament building, which the police had not yet entered since the occupation began on Tuesday.
The students criticised the police tactics and vowed to keep protesting against what they said are illegal moves by the ruling party to ratify a contentious trade agreement with China.
Prime Minister Jiang Yi-huah condemned the protesters for breaking into government buildings, the state-run Central News Agency reported.
“We express great sorrow about the plot to break in the cabinet. The student movement has gone too far,” Jiang said after meeting with President Ma Ying-jeou early on Monday.
About 5 000 baton-wielding riot police spent five hours dispersing thousands of protesters, mainly students, from around the cabinet building.
Police arrested 61 student leaders, most of them members of National Tsing Hua University-based Black Island Nation Youth Front.
The Taipei city government said the injured include 109 protesters and 52 police officers injured.
Jiang defended the police action to disperse demonstrators occupying the cabinet building.
He also urged students inside the legislative chamber to leave and exchange opinions with him without setting conditions first.
Thousands of demonstrators remained outside the legislative building on Monday.
Hundred of students occupying the legislative chamber vowed to adopt non-violent resistance if the police began to clear them out.
The protesters called on the government to withdraw the trade bill from parliament and enact new regulations on oversight of cross-Strait agreements signed with Beijing.
The pact, signed last June by Taipei and Beijing, is awaiting ratification by Taiwan's legislature.
Critics say China will have too much influence on the island's economy if the pact is adopted.
Jiang and Ma rejected protesters' demands over the weekend.
Ma said failure to ratify the pact would compromise Taiwan international credibility and hurt its economic development.
National Security Bureau director Tsai Der-sheng resigned on Monday amid the turmoil.
The Association of Taiwan Journalists also denounced police for preventing reporters from covering the protest.
It alleged that dozens of journalists on the scene were violently ejected from the area by police prior to the clearing operation at the cabinet building. - Sapa-dpa