Catholic principals are refusing to distribute a letter that warns parents against voting for the Greens in the upcoming federal election.

It came as the Greens hit back at the Catholic Education Commission of Victoria, accusing it of ignoring the best interest of students and Catholic teachings.

The Commission wrote to tens of thousands of Victorian parents last week, claiming that the Greens' education policies would result in less funding for Catholic students and potentially higher school fees.

But in a fiery letter to the Commission's executive director Stephen Elder, Greens education spokesman Nick McKim said the party's backing of the Gonski school funding reforms and its pledge to invest $4.8 billion over four years to support students with a disability would benefit Catholic students.

Principals and school leaders have contacted the Greens, saying that they will not pass on Mr Elder's letter to students and parents.

"Perhaps that is because they understand that your letter is motivated far more by your close association with the Liberal Party than it is by a desire to act in the best interests of students at Catholic school and their parents," Senator McKim said.

One Catholic principal said he refused to circulate the letter because it was not the role of a school to tell parents how to vote.

"I respect the adults in our school community to make up their own mind about who to vote for," he told The Age.

"I didn't see the point in us telling parents how to vote. I am sure they have made up their own minds already."

The Greens have called on the Commission to send another letter to families correcting its "misleading comments".

Senator McKim said the Greens' policies on asylum seekers, global warming and the environment were more consistent with Catholic teachings than the major parties' policies.

Mr Elder stood by his previous comments, and said the Greens would strip funding from non-government schools and repel religious exemptions for employment.

"His party would seek to gut our schools because the Greens perceive that funding for our schools has had, quote 'an adverse impact on public education.' So the Senator needs to get his stories straight," he said.

He said the Greens had ignored his requests to clarify its education policies.

Mr Elder sent the letter to 100 schools in marginal seats, seats where MPs are retiring and electorates where the Greens are hoping for a win.

The letter attacked the Greens' model because in addition to basing funding on socio-economic measures, it would consider a school's resources and its ability to generate income from other sources.

It also criticised the Greens for seeking to "abolish our ability to hire staff on religious grounds".