While the limit on funerals has been increased from 10 people to 50, there's no change for other religious gatherings meaning weekly services and prayers are still unable to go ahead under alert level 2.
Many religious leaders are disappointed that 100 people can gather in a restaurant or bar but not at a place of worship.
COVID-19 has forced weekly mass, prayers, and other religious services online.
But under alert level 2 faith leaders had hoped they would be able to open their doors once again.
Ikhlaq Kashkari, the New Zealand Muslim Association president, says he is "very disappointed".
"The community is very distraught, particularly because this is a month of Ramadan and we were hoping for the last ten days at least we can attend the mosque," he told Newshub.
Kashkari says the 10 person limit on religious gatherings came as a shock because he had carefully outlined his health and safety plans to the Government.
They included worshippers bringing their own prayer mat, CCTV, and an online booking system to keep numbers under 100.
"Then you take something like a restaurant, or even a game of rugby where people have contact and that's allowed and we're not allowed," he said.
The 100-person party at Auckland viaduct bar Headquarters this Friday has also upset church leaders who are trying to sell their communities on the restrictions.
The Minister of Commoners Weslyan Methodist Community Reverend Frank Ritchie says it's inconsistent.
"I'm struggling seeing that when I have a full health and safety plan in place for my church to be able to engage within the rules and we can't do it, so whilst I get it, I struggle with what feels like some inconsistency."
More than 300 Catholic churches across the country will open for people to pray privately from tomorrow - provided less than 10 are present.
But Destiny Church leader Brian Tamaki told The AM Show he's going ahead with a normal service this weekend despite it breaking the rules.
"We're going to have service this week and obey the rules, and do the social distancing, but we're not going to give up our freedoms any longer," he said.
His plans have been dismissed by the Prime Minister.
"We want him to listen to public advice in the same way we want everyone to," said Jacinda Ardern.
"No one wants to risk an outbreak and I'm sure he wouldn't want to put his congregation at risk. "