Māori communities are deeply concerned that police may be able to search marae and homes without a warrant when the alert levels drop.
It is another contentious aspect of the Covid-19 Health Response Bill, which is being rushed under urgency through Parliament.
After backlash from Māori leaders and communities, the government has removed a reference to marae from the legislation.
But Prime Minister Jacinda Ardern said the reference to marae gave them extra protection.
"What the Bill explicitly did was actually make sure that rather than marae being treated potentially as commercial premises, where there are wider powers, to actually narrow it and make sure they had the same protection as private dwellings," she said.
"That was the intent so that there was no question and that they had that higher - there was that distinction in there.
"But after concerns were raised, there was no question that we would rather respond to that."
This morning, Māori-Crown Relations Minister Kelvin Davis said the reference to marae would be removed.
Marae will now be treated the same as any other dwelling, which means officers can search marae without a warrant if they believe that someone is breaking the rules of the alert levels.
Beforehand, officers could only search marae without a warrant if that entry was also necessary to give direction to stop any activity of non-compliance.
Davis was not happy with the change.
"Māoridom has to be careful what they wish for - that's the problem," he said.
"What this now does is it reduces the protections that were being afforded to marae... our intention was to give marae the best protection that we possibly could.
"We have heard the concerns and we have listened to Māori who think that marae are being particularly targeted and we have made the changes."
However, Māori Council executive director Matt Tukaki - who pushed to have the word marae removed - said it needed to go.
"The use of the word marae did not need to be there, it denotes a single race and it denotes a single culture," he said.
However, he said he did not intend for that to strip the protections around marae.
He said there had been several amendments and definition changes to the legislation in the past 24 hours, and it remained confusing.
"What they have done is they have shifted words and meanings around," Tukaki said.
"Now, when you really think about it in its entirety, it needs to be open to judicial review."
Another amendment was made today to ensure a marae committee is notified after a warrantless search is carried out.
That is hardly of comfort to the chair of Te Puea Marae in Auckland Hurimoana Dennis, who said the rules were over the top.
"It sort of flies in the face of the relationships that the police and every other government agencies have with their local marae," he said.
"Any sort of search should have been consensual. There really should have been no issue at all."
Dennis said they had a trusting relationships with police iwi liaison offices, and they should be the only ones that deal with marae in these circumstances.
The bill has been under urgent debate in Parliament today after last night passing its first and second readings.
The Human Rights Commission said it was deeply concerned that the bill had been rushed with a lack of scrutiny, and added that the bill must honour Te Tiriti o Waitangi.
Justice advocate Julia Whaipooti agreed the rushed process was a concern, as was the power police would have if it was passed.
"Understandably, we are in a strange time in this pandemic time, so they need to allow for more powers," she said.
"But it needs to be proportionate to what is happening at the moment and we know that police use powers disproportionately against Māori.
"It is something for us to be very concerned of."
Whaipooti has encouraged people on social media to change their profile picture to a symbol of a fist clenching a feather.
In a post being circulated on Facebook, she said the symbol represents solidarity and respect for Māori - something she said had been lost with the government's latest announcements.