The Greens have accused the Catholic school lobby of trying to protect its "special" funding deal with the federal government after letters were sent to parents suggesting they shouldn't vote for the minor party.
The Sydney Catholic archdiocese's education arm has written to parents on the eve of the federal election warning the Greens are pitting the government and Catholic schools against each other.
Sydney Catholic Schools argues the outcome of Saturday's vote will be critical for families with children in Catholic schools.
"Of primary importance to Catholic education is the ongoing affordability of our schools to Australian families who seek a Catholic schooling for their children," the organisation's executive director, Tony Farley, writes in the letter seen by AAP.
He suggests that while the coalition and Labor would keep non-government schools affordable the Greens have publicly called for funding levels to be cut.
"We ask you to keep this in mind when you vote on Saturday."
One parent who received the letter said matters of church and state should be kept separate.
"I think they should be spending more time educating kids and less time telling people how to vote," the parent told AAP.
The Greens argue increased funding to non-government schools has had a negative impact on public education.
The party says any funding to non-government schools shouldn't advantage private education "at the expense of public education".
It wants private school funding scaled back in line with the commonwealth's schools resource standard (SRS) and any monies freed up to be re-invested in public schools with the highest need.
Greens education spokeswoman Mehreen Faruqi says the Catholic school lobby has historically been overfunded and is now "trying to protect their special deals".
"I won't apologise for standing up for disadvantaged public schools that have been chronically underfunded by governments of both stripes who refuse to stand up to cashed-up lobby groups," Senator Faruqi said in a statement on Friday.
Some 99 per cent of public schools are underfunded while the same percentage of non-government schools are funded at or above the SRS, Ms Faruqi said.