Two of Destiny Church's biggest charities may be set to be stripped of their tax-exempt status by the Department of Internal Affairs after failing to file their annual returns on time.

The two charities, which are central to the business operations of the church headed by controversial pastor Brian Tamaki, have been told they will be removed from the Charities Register if they do not file returns within 20 working days.

Internal Affairs said the Destiny International Trust and Te Hahi o Nga Matamua Holdings have been sent a Notice of Intention to Remove from the Register for failing to file the required annual returns. This was standard practice.

"They now have 20 working days to file an objection to the notice, or file both overdue returns, or they will be removed from the register."

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But church spokeswoman Anne Williamson told the Herald the church was confident neither charity would be deregistered.

"We've been given an early November deadline and we're confident we're going to be able to make that."

She said the delay was due to new Charities Commission criteria.

"As with every charity this time round I suppose, getting into the audit, it's not until you commence that you find out whether you have to go up a tier," she said.

"We're working with a very reputable auditor who's being very thorough. We're very happy with the process.

"We did a lot of work beforehand on preparation but it's not till you get in that sometimes you find out exactly how you're being assessed. We're on our journey and we're confident we'll meet the deadline."

She would not reveal the name of the auditor.

Both charities were given a stern warning in December last year after failing to file their annual returns.

At the time Destiny Church said the delay was because it was proving difficult to find an auditor.

The church was already facing scrutiny from Charities Services - an arm of Internal Affairs - which indicated in November it would be analysing the church's tax-free status after receiving a complaint from the public that it was breaching the Charities Act.

Internal Affairs said it had received a filing from a third Destiny charity, the Destiny Church Auckland Trust.