Baker, the former leader of the New Conservatives, was previously charged with trespassing on Parliament grounds and resisting police.
The charges were laid after the 23-day occupation erupted into a violent riot on the front lawn of Parliament in early March.
Considered one of the main faces of the protest, Baker told The New Zealand Herald he was pleased the charges against him had been dropped, though he did not yet know why.
"That's pretty well it, really. They just withdrew all the charges. That's all I got from my barrister," he said.
He was "pretty happy about it" and said he struggled to see how police could continue pushing the charges, especially as many other protesters had their charges withdrawn as well.
Baker said he didn't commit any of the crimes he was accused of, saying the charge of resisting police was "bizarre".
"I didn't resist them one little bit."
He was "pleased they've seen sense".
"There was no criminal offending going on. Innocent people shouldn't be charged."
Baker said when he was arrested there were about 30 to 40 other men in the holding cells who were about the same age as him.
"I think only one of them had ever been in a holding cell before in their lives, so that just proves it was average Joes . . . to arrest that many in that situation, there's something wrong."
Police have been contacted for comment on the withdrawal.
Baker reportedly represented a raft of groups involved in the protest, working as a liaison between those protesting and Parliament officials.
Groups Baker advocated for included The Freedom Alliance, New Zealand Doctors Speaking Out with Science, Outdoors & Freedom Movement, The Freedoms and Rights Coalition and Voices for Freedom.
A police operation brought the 23-day demonstration to an end in March, after anti-mandate protesters gridlocked central Wellington streets and constructed a tent occupation outside Parliament.
It came to a violent end after police moved in on protesters, and a fire was started on Parliament's lawn.
As well as the ongoing police investigation, the Independent Police Conduct Authority is investigating the policing of the anti-vaccine mandate protests.
In June, more than a third of police involved in the protest response had been referred to wellness advisors or psychologists to help deal with the emotional toll of the experience.
Information released under the Official Information Act showed officers were hospitalised after being hit in the head with bricks, sprayed in the face with substances, and suffering dislocated shoulders and torn tendons.
