The charities regulator has threatened the tax-free status of the Catholic Education Commission of Victoria (CECV) after it urged parents not to vote for the Greens at the federal election.

Key points: CECV executive director wrote to parents/carers about "highly problematic" Green's policy for Catholic schools

CECV executive director wrote to parents/carers about "highly problematic" Green's policy for Catholic schools In response to reports, charities regulator wrote to the CECV

In response to reports, charities regulator wrote to the CECV Concerns received by ACNC during and following 2016 Federal Election campaign significantly higher, Murray Baird says

The Church responded by accusing the regulator of mounting "a fishing expedition predicated on hearsay derived from third-party media reports".

The exchange of letters has been obtained by the ABC and comes amid an animated debate in the Coalition about the charitable status of groups like the Australian Conservation Foundation and Environment Victoria, both of which campaigned against Liberal candidates in the July poll.

Neither group received a similar "please explain" from the Australian Charities and Not for Profit Commission (ACNC), despite Coalition concerns they had engaged in campaigning against them.

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Before the election, the ACNC renewed its advice to charities and not for profits about engaging in political activities.

The brawl between Church and regulator began with a June 23 letter from the executive director of the CECV, who wrote to parents and carers about federal funding.

Stephen Elder said the Greens' policy on Catholic schools was "highly problematic".

While the Greens supported needs-based funding, the letter asserted the party's policies would undermine its schools' funding, ability to teach disadvantaged students and hire on religious grounds.

"At its worst, principals and school leaders would be forced to employ staff who could be openly critical of our faith, and be able express those opinions in our schools," Mr Elder said.

It concluded by saying there was a real chance the Greens could hold the balance of power in Parliament after the election, "which could put commitments from the major parties at risk".

"When you balance what's really important to you at the ballot box, please remember that both Labor and the Liberals are committed to secure any ongoing funding for local Catholic schools like yours," he said.

A fortnight later the charities regulator wrote to the CECV citing media reports about the letter to parents and pointing to the regulator's guidance on political campaigning.

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"We are concerned to ensure that that activities of the CECV are not placing the charity at risk of being found to have a disqualifying purpose and therefore affect the charity's entitlement to registration as a charity," ACNC director of compliance Prue Monument wrote.

The ACNC was unable to comment about the exact nature of its ongoing investigations due to secrecy provisions in the legislation that sets out how the Commission is run.

However, Assistant Commissioner Murray Baird issued a statement to the ABC saying "a number of concerns about registered charities engaged in political advocacy" were received by the ACNC during the election campaign and in the following weeks.

"The number of concerns received by the ACNC during and following the 2016 federal election campaign was significantly higher than the number received during and following the 2013 federal election campaign," Mr Baird said.

"The ACNC reviewed these concerns and subsequently contacted a number of registered charities.

"Some of these reviews are ongoing, and the ACNC will take action where appropriate."

Mr Baird said his organisation receives an average of 60 complaints per month, with each one taken seriously and reviewed before any further action is taken.

Both the ACF and Environment Victoria have confirmed to the ABC that the regulator had not raised any concerns about their activities during the campaign.

CECV has issued a statement saying it's actions were "expressly permitted under the provisions of the Charities Act 2013".

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