Taiwan riot police have used water cannon to disperse hundreds of demonstrators who had stormed government headquarters, protesting against a controversial China trade pact.

A total of 1,000 police officers were deployed on Monday to remove the protesters from the cabinet headquarters, the prime minister's office said, adding that at least 61 people were arrested.

Clashes broke out after riot police tried to remove protesters from government buildings and compounds that they had broken into. The police eventually managed to clear out the buildings by using water cannons. 

National Taiwan University Hospital which is located near the government headquarters said it had treated 57 injured people and police officers since late Sunday.

One protester told Al Jazeera that their protest was not over, despite Sunday's failed occupation, as another government building occupied last week was still under their control.

"It's not the end of the movement at all," said Jiho Tiun, a student at National Chen Chi University, who added that the secrecy surrounding the signing of the pact and China's influence were the main reasons behind the demonstrations.

Signed in June by representatives from Taipei and Beijing, the pact is still awaiting ratification by Taiwan's parliament. It would open dozens of service sector industries in each side's territory to companies from the other.

Tens of thousands of people have flocked to the area around parliament in recent days, in the sternest test so far for President Ma Ying-jeou's six-year effort to bring Taiwan's economy closer to China's.

"The government denounces violence and dispersed the crowd according to the law. We will not tolerate actions designed to paralyse the government," the presidential office said in a statement.

Source: Al Jazeera and agencies