A total of 1,000 officers were deployed overnight to remove the protesters from the Executive Yuan where the cabinet is located, Taipei's police department said, adding that 32 people were arrested.
In wild scenes, demonstrators pulled down barbed wire barricades surrounding the government building, and used ladders to break into offices on the second floor.
Clashes broke out when police tried to remove the protesters from the building and the compound surrounding it, with many lying on the ground with their hands linked to try to defy efforts to shift them.
Police used riot shields to push the crowds back while some of the demonstrators tried to grab their batons and pelted them with plastic bottles. Two water cannon trucks were then deployed, eventually subduing the crowd and clearing the building.
One injured male protester lay on the ground, attended to by medical personnel while another was led away with blood streaming down his face, AFP journalists saw.
Taiwan's TVBS news channel said around 120 people were injured in the clashes, but police were not immediately able to confirm the figure.
National Taiwan University Hospital which is located near the government headquarters said it had treated 57 injured people and police officers since late Sunday.
The protesters, who occupied the nearby parliament last Tuesday, are opposed to a pact with China which 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 Taiwan's ruling Kuomintang party.