Around 900 people gathered at the city's harbourfront government complex with some trying to force their way into the building to oppose the project, which they say will displace villagers and turn farmland into housing estates -- favouring property developers.
Television footage showed protesters pushing over barricades and surging towards an entrance to the Legislative Council as lawmakers met to discuss funding for the development.
Police cordons inside and outside the building pushed back the rally late Friday as protesters tried to prise the doors open with bamboo sticks, shouting "Withdraw the plan".
They managed to smash a hole in a glass panel, which police inside then used to pepper-spray protesters, while lawmakers were forced to suspend the meeting.
Around 200 protesters then chained themselves together for a sit-in outside the building and anti-riot police were sent in to disperse them and make the arrests.
A police spokesman said a "minimal level of force" was used to handle the protest.
He added police had acted to remove the protesters upon a request from the Legislative Council -- the city's top lawmaking body.
Jasper Tsang, speaker of the Legislative Council, condemned the protest.
"We feel very regretful that some people disrupted the committee meeting of the Legislative Council through such means," he told reporters on Saturday.
Hong Kong suffers from a serious shortage of housing and government leader Leung Chun-ying made increasing supply a policy priority when he took office in 2012.
He hopes to cool record-high housing prices, which have rocketed due to an influx of investment from mainland China.
But concerns have been raised that the new housing projects threaten the city's nature reserves and will encroach on its country parks.