Protesters fought police armed with pepper spray, batons and water hoses on roads around the camp in Admiralty.
Police say 40 people have been arrested and a number of officers were injured.
The protesters want the people of Hong Kong to be allowed to choose their leaders in the 2017 elections without interference from Beijing.
The Chinese government has said it will allow universal suffrage, but will screen candidates for the chief executive post in advance.
Last week police and court bailiffs removed one of the major protest camps in the Mong Kok commercial district.
The protesters had public support at the beginning, but that is now ebbing as many Hong Kong residents believe the protests are causing too much disruption.
The unrest flared late on November 30, after student protest leaders called on supporters to converge on the offices of Chief Executive CY Leung on Lung Wo Road.
The road is a short distance away from Connaught Road in Admiralty, the major road protesters have been occupying for two months.
Protesters, many wearing hard hats and carrying umbrellas – the symbol of their movement – moved into the area, throwing bottles, helmets and umbrellas towards police.
Police ordered them to retreat, then charged protesters, eventually forcing them out of the area. Police sprayed water to disperse protesters, in addition to batons and pepper spray.
On December 1, government offices were shut and staff were told to stay home. But the roads outside the government site were clear of protesters and open for traffic.
By afternoon government employees were able to go back to work.
The atmosphere remains tense at Connaught Road where hundreds of protesters are still occupying the area amid a police presence.
Hong Kong’s security secretary, Lai Tung-kwow, has blamed students for escalating violent behavior, and defended the use of force by police.
“The police have to take resolute actions, they have no choice … it is their duty to restore law and order,” Lai Tung-kwow told reporters at a press conference on December 1.
Last week more than 100 people – including some key protest leaders – were arrested as the Mong Kok camp, across the harbor from Admiralty, was dismantled.
The latest clashes come after China said it would not allow a UK parliamentary committee to enter Hong Kong as part of an inquiry into British relations with its former colony.
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