Church leaders across the country are facing a dilemma around how they will deal with unvaccinated people within their congregations.

It comes as the conversation around mandatory vaccinations heats up.

Earlier this week the Government announced digital vaccination certificates, which should be introduced by November.

More details are expected in the coming weeks, but for now, the certificates will be used as a tool in high-risk settings including large events and festivals, and the Government is consulting on their use in places like hospitality.

It will not be used for places like supermarkets or essential health services. It will be available either in digital form on smartphones or can be downloaded and printed out.

Auckland Church Leaders Group Chair Jonathan Dove said it's a contentious issue.

"We are in a very challenging situation because churches tend to meet indoors and we sing and hug, and those are all things that spread the virus."

But Dove said regardless, churches should be assisting not dividing in the fight against Covid-19.

"Churches need to take the virus seriously and should be proactively implementing health measures."

"Yes, we are in a difficult position, but that's because of the virus, not the Government," Dove said.

Dove, who is also the Senior Pastor at Auckland's Grace City Church, said they are looking at options around how church services will be held once the government deems it is safe to do so again.

"We are exploring whether to provide separate services for vaccinated and unvaccinated church members," Dove said.

St Peter's Anglican Church in Wellington hasn't yet settled on its response to vaccinated and unvaccinated church members.

Reverend Stephen King said the situation is like trying to balance along a tightrope.

"We are encouraging people to get vaccinated, but we don't want to make it a pre-requisite in order to belong to the church."

King said church services will inevitably have to change as the Government has moved away from its elimination strategy.

"Churches now need to find a way to meet the needs of those who are jabbed and those who refuse to be, because the risk of Covid is out there."

"There are some churches that are quite happy to tell people what to do, but we are having that conversation now with our members and leadership," King said.

City Impact Church has locations across New Zealand. Its leader Peter Mortlock was recently called out for encouraging members to attend Brian Tamaki's Destiny Church-led anti-lockdown protest last Saturday.

As many as 2000 anti-lockdown protesters gathered, including families with young babies.

Brian Tamaki's confirmed he's been charged in relation to the event and intends to defend his actions.

Mortlock said he was asked to be involved in the rally but had taken a back seat in it.

In a statement, Mortlock said City Impact takes no official nor ethical stance on the use of vaccines.

"City Impact Church has always been very supportive of and endeavours to comply fully with the public health measures implemented since the pandemic started."

But Mortlock also said the church strongly objects to any legislation or government restrictions that would limit in-person church attendance based on vaccination status or any other status.

"Our church has always been open to everyone, without discrimination. Such restrictions would have a major impact on the mental, emotional and social health and wellbeing of thousands of people who call City Impact Church their church."

Meanwhile across the ditch, Australia's two largest cities are facing tough restrictions for returning to church services.

Sydney and Melbourne have been in a difficult lockdown for months, after an outbreak in June in Sydney eventually made its way to Melbourne.

New South Wales' rules require that in the first stage of return to church when 70 per cent of the adult population is fully vaccinated, only those fully jabbed will be allowed to attend.

In Victoria, Melbourne churches will need to have different congregation sizes, depending on vaccination levels.