As restrictions have eased over the last couple of weeks, pubs and clubs are planning to welcome more patrons.
But churches have not been given the green light to welcome anymore than 10 worshipers.
When asked about the comments, Armidale's Anglican Bishop Rick Lewers said he did not believe churches were being unfairly treated by the government.
"If I was in America I'd be really uptight about that, because I think there is a religious freedom issue," Bishop Lewers said.
But here he said their aim as a church was to be compliant and helpful.
"I don't think our Prime Minister is trying to pick on religious groups unnecessarily, but the thing we do have to watch as a church, I believe, is (that) there there isn't one rule for the general public and another rule for religious groups, because religious groups are part of the general public."
While Catholic Bishop Michael Kennedy admitted he was disappointed, when The Express asked him about the discrepancy between pubs and churches, he was hopeful it would soon change.
"I think we're just as safe in the church as we are elsewhere, but we'll abide by what decisions are made," Bishop Kennedy said.
He said he hoped they could soon have more people inside churches if more restrictions were eased later this week, but if not he said he would be disappointed.
"I don't want to be critical of the government, I think they've done a fantastic job," the bishop said.
"Our pubs and clubs are not yet allowed to have 50 people, and so they're the same as the churches at the moment."
Bishop Kennedy said they had been open for the past two weekends for mass.
"We've had to do it by people contacting their local parish to book in for a day and time," he said.
"You can tell their mood when they come along, especially when they come along for their first one after being locked out of the church for so long, was very joyful.
"It's really been appreciated by the people, being able to come along and worship together, even in small groups it's been a real turning point.
He said they were hoping there might be another easing of restrictions next month that would allow more people to attend.
In the meantime the church has been live-streaming services recorded at the Armidale cathedral.
Bishop Lewers said all Anglican church services in the region had remained closed due to the restrictions.
Once further restrictions were lifted he said they would start to look at smaller churchers opening along with bible study classes.
The Catholic service has been livestreamed online since early April, which Bishop Kennedy said had attracted plenty of interest. But he noted most people watch it later rather than watching it live on Sunday mornings.
"Some people do joke with me they do that so can fast forward through my sermon," he laughed.