The head of the Catholic Education Commission of Victoria, Stephen Elder, has lashed out at the Greens, accusing the party of being anti-Christian.

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In comes after Greens leader Richard Di Natale called on the charities watchdog to revisit its decision not to withdraw the Catholic Education Commission of Victoria's charitable status for urging Catholic school parents not to vote for his party at the federal election.

"Richard Di Natale leads a party that's prepared to dump on a whole raft of issues on Christian and Catholic Churches," Mr Elder said.

"And when his party's policy to de-fund Catholic Schools at the last federal election is critiqued he responds like a petulant school boy."

In June Mr Elder issued a circular to the parents and carers of Victoria's Catholic students, critiquing the Greens' education policies.

It said they threatened Catholic school funding and the ability of schools to hire staff on religious grounds.

It urged parents to "balance what's really important to you at the ballot box".

That drew a "please explain" from the Australian Charities and Not For Profits Commission (ACNC), which said the Church might have breached rules on political campaigning and that might "affect the charity's entitlement to the registration as a charity".

Mr Elder, who is a former state Liberal MP, disputed he had broken the rules and the commission took no further action.

At a Senate Estimates Hearing yesterday, Senator Di Natale asked Charities Commissioner Susan Pascoe if that decision could be appealed against.

"How is advocating not to vote for a political party inconsistent with the purpose of opposing a political party?" Senator Di Natale said.

"Can we perhaps put on the record that we will be requesting to be an official complainant in this specific instance, and we're waiting to hear from you on notice whether there is any capacity to review the decision."

Mr Elder said he would be failing his duty to parents if he did not critique the policies of political parties and he would not be intimidated.

He called on the Greens to recast the party's policies on religious schools.

"Otherwise they will continue to alienate the 65 per cent of Australians who are Christian and the 38 per cent of students who are educated in Catholic and independent schools," he said.

Asked if he believed the Greens were anti-Catholic and anti-Christian, Mr Elder said the party's bias against Catholic school was evident in its education policy.

"They have a real problem with us and when we try to engage to get the detail about it, they won't talk to us," he said.

"I'm not telling our parents how to vote, I'm telling them 'this is the impact of their policies'."

Senator Di Natale said his party was still "concerned about the misleading impact that the Catholic Education Commission's letters had on voters".

"If implemented, our election commitments would have delivered more funding to schools, including Catholic schools in need, than either the Liberal coalition or the Labor party," he told ABC News.

Coalition Senators raised concerns in estimates yesterday that the Charities Commission had not issued a please explain to groups like the Australian Conservation Foundation, despite evidence it had campaigned against Liberal candidates in the July poll.