Clashes have broken out between pro-democracy demonstrators and police in Hong Kong as Occupy activists attempted to storm the government headquarters in Admiralty targeting Chief Executive Leung Chun-ying's office.

Stepping up their campaign for fair and free elections in the semi-autonomous region, hundreds of protests tried to lay siege to the building overnight.

Security personnel used pepper spray and batons to disperse the crowd but the unrest spilled over into Monday morning disrupting commuters.

Police are clearing road-blocks and demolishing tents erected by the activists.

The demonstrators marched on the headquarters wearing masks, hard hats and umbrellas, which have become the symbol of the movement.

Many police officers are said to have been injured in the skirmishes. At least 45 protesters have been arrested. This is one of the worst outbreaks of violence since protesters took to the streets of Hong Kong's financial district.

"I urge everyone to stay here until the morning to keep surrounding the government headquarters. Let's stop the government from functioning tomorrow," an activist was heard shouting using a loudhailer, reports Reuters.

The latest flare-up comes just hours after a stern warning from police to the protesters to desist from illegal activities so as to avoid "giving the police a legitimate reason to take violent actions".

A spokesperson for the Heads of the Universities Committee asked the protesters to remain calm and advised them against storming the government headquarters.

A statement said: "Please do not take part in any attack against the government headquarters. Stay away from areas where there are clashes. Evacuate from the site immediately if your personal safety is in danger. Please contact your respective institution for help if needed."

About 3,000 police personnel have been deployed in Admiralty and nearly 4,000 in the Mong Kok, another district where violence erupted overnight.