Police say it's "extremely disappointing" arrests had to be made after some protesters attempted to push past a line of officers and enter Parliament on Wednesday afternoon.
The arrests came as the second day of protests, which had been previously peaceful, escalated into aggressive behaviour by some.
The protest escalated shortly after 3pm on Wednesday as protesters swarmed Parliament grounds. Video showed one man addressing the crowd before turning and facing the police, as police could be seen pushing one protester back.
The crowd then began to chant "let them through" before the protesters begin trying to push through the police line, with officers pushing back.
The man who had addressed the crowd was the first of three protesters to be arrested.
As tensions escalated, some in the crowd heckled and verbally abused media. By 4pm the crowd had settled down and had largely dispersed, but a strong police presence remained.
Wellington District Commander Superintendent Corrie Parnell told 1News "police have this afternoon arrested three people on the grounds of Parliament after they attempted to breach the police line".
"This is extremely disappointing as until this occurred, the activity of most of those present has been peaceful for the majority of the day.
"Police will maintain a presence at Parliament tonight and will continue to monitor activity recognising that people had a right to peaceful protest.
"Police remind the public that there will continue to be some disruption to traffic flows in central Wellington, and motorists should allow extra time as delays are likely this evening and tomorrow (Thursday) morning. For the most part, traffic around the city is largely free-flowing."
A small part of Molesworth Street remains impassable to through traffic and the area around Parliament, including the northern end of Lambton Quay and lower Bowen Street, should be avoided and alternate routes sought.
Corrie said anyone with any specific concerns in relation to the protest activity should contact Police via 105.
On Wednesday morning, Speaker Mallard told 1News a note was given to the protesters on Tuesday night to say that it's against the rules to pitch a tent on Parliament grounds and that they will be liable for trespassing if they remain there.
Several cars and trucks were continuing to block roads around Parliament grounds with disruptions to some bus services.
Around 1000 people attended protests on Tuesday, after convoys travelled to the capital from around the country.