Police Commissioner Andrew Coster says a team of staff working at the protest have caught Covid-19 and while it hasn't been linked to protesters, it "stands to reason" the coronavirus is there.
Coster told Morning Report today even if the virus was not at the protest "it will be soon".
Asked if there was pressure on police to deal with the protest before the Omicron outbreak expanded, Coster said Covid-19 was just one of part of the situation.
"I'm concerned for the city, I'm concerned for the university with students coming back, I'm concerned for the operation of public transport, so there's all of that.
"Then there's a bigger picture here, which is a range of protests happening around the country. At this stage they are peaceful and they're not blocking critical infrastructure, but we need to appreciate that the overseas experience has been a lot worse than ours, so it's a delicate situation that needs to a measured response."
Police had "hundreds" of officers working on the protest and numbers would remain high over coming days.
"It stands to reason that Covid will be there and if it's not it will be soon because it's increasing" - Police Commissioner Andrew Coster
As for officers who were sprayed with a stinging substance yesterday, they were doing well this morning, Coster said.
Police were still investigating what the substance was.
It was one of the actions used against police - protesters have also thrown human faeces at them.
"I'm really concerned for their safety and incredibly proud of the job they're doing in very difficult conditions," Coster said.
The environment at the protest was making it difficult to police and less safe, he said.
"It's a dynamic situation but our focus remains on returning as much of the city to normal as we can, as quickly as we can."
Asked if police would work with protesters to identify people causing issues, Coster said that was "completely unrealistic".
"This is a crowd situation - we aren't going to go in there and pluck out individuals. We need the whole situation to be returned to a state of lawfulness, and that looks like giving back the areas that Wellington needs to get on with its life and it looks like enabling a situation where normal police patrolling can occur within the grounds of Parliament and that is the answer to those safety problems."
The situation was enabling the problematic behaviour, and police were "not seeing anywhere near enough movement towards an attempt to make this protest lawful".
"Until we do, you know, it's really on them to sort it out."