About 100 demonstrators were detained at an energy ministry complex on charges of violating a state of emergency, National Security Council chief Paradorn Pattanatabut told AFP.
"There was no resistance," he said. "They were overwhelmed by the police forces."
It is the first time such a large number of protesters have been arrested since mass rallies seeking to overthrow Prime Minister Yingluck Shinawatra began more than three months ago.
Mr Paradorn said demonstrators had also agreed to reopen roads into another government complex in the northern outskirts of Bangkok to enable officials to return to work.
Riot police with batons, shields and helmets were also deployed near the government headquarters, after protesters returned to areas around the complex following a similar police operation on Friday to reclaim the building.
On Monday, demonstrators poured buckets of cement onto a sandbag wall in front of a gate to Government House.
The protesters are demanding Yingluck resign and hand power to a temporary, unelected government that would carry out reforms to tackle corruption and alleged misuse of public funds before new elections are held.
Yingluck's government held a general election on February 2 in an attempt to defuse tensions, but the opposition boycotted the vote, saying it would not end the kingdom's long-running political crisis.
Her opponents say she is a puppet for her brother Thaksin Shinawatra, a billionaire tycoon-turned-premier who was ousted in a military coup more than seven years ago and fled overseas in 2008 to avoid jail for a corruption conviction.
The video and photo gallery above capture the events surrounding the anti-government protests in Bangkok on Tuesday, Feb 18, 2014. (Bangkok Post video and photos)