Witnesses say tear gas was fired as scuffles broke out and at least 15 protesters have been arrested.
"They won't allow us to send a new group of police," Lieutenant-General Akerach Meepreecha of the Metropolitan police said.
The protesters have been camped out on the grounds of Samak Sundaravej's office in Bangkok since Tuesday.
Demonstrators led by the People's Alliance for Democracy (PAD) formed a human chain on Friday around five protest leaders who have been demanding the resignation of the present government.
|The crowd formed a human chain to force police out of the compound [EPA]
The alliance is seeking to force the resignation of Samak and his cabinet, claiming they are corrupt and serving as a proxy for Thaksin Shinawatra, the former PM who was ousted in a 2006 coup and facing several corruption charges, has gone into exile in London.
Police appeared to exercise restraint when the protesters, some armed with golf clubs, batons and bamboo sticks, forced 400 personnel out of the
Government House grounds just after midnight.
Al Jazeera's Selina Downes reporting from Bangkok says the crowd appeared to be provoking police action but the government was still withholding the use of force.
Samak and police officials have repeatedly said that force will not be used to remove the thousands of protesters from the compound of the government building.
Police Lieutenant General Suraphol Thuanthong had earlier said that they will use a "softened stance" to deal with the protesters.
"We will give them time to leave the government house. But if they continue to defy the court order, then we have to use force to drive them out," he said.
"I cannot set the precise time or deadline for this."
Al Jazeera's correspondent said police would be trying doubly hard to disperse the crowd before more protesters come into the capital from the countryside over the weekend, as has been the case for three months of protest.
The protests appeared to be spreading on Friday, with about five thousand protesters blocking Phuket international airport, an official said.
There were also reports of a similar blockade at Krabi.
Early this week protesters numbering up to 35,000 at their peak vowed to remain camped at Government House in their "final war" against Samak until he resigned.