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Catholic education authorities are short-changing needy schools by up to $1.5 million a year to help keep fees low at schools in wealthy areas in Sydney and Melbourne, government data reveals.
The release of the previously secret Department of Education data comes as the peak body representing independent Christian schools called on the Catholic sector to stop campaigning against the government and support its school funding "breakthrough".
The Turnbull government will introduce its school funding changes into the House of Representatives for debate on Tuesday.
The federal government funds Catholic schools on a needs basis but distributes the money to state and territory education commissions in a lump sum, which they distribute among schools as they see fit.
St Mary of the Cross MacKillop Catholic Parish Primary School, a low-SES school in Melbourne's Epping North, received $1.86 million in 2015 - $1.49 million less than its federal government allocation.
The most socially disadvantaged Catholic school in Victoria, St Thomas Aquinas in Norlane, received 15 per cent less than its federal government funding allocation in 2015.
Meanwhile, St Columba's School in the affluent Melbourne suburb of Elwood received 15 per cent more funding than its federal government allocation.
St Jerome's Catholic Primary School, a low socio-economic school in the western Sydney suburb of Punchbowl, received $2.71 million in funding in 2015 - $1.3 million less than its federal needs-based entitlement.
By contrast, Sacred Heart Catholic Primary School in Pymble received $412,500 more than its federal funding allocation.
Education Minister Simon Birmingham on Monday said: "I think people would be very concerned if they thought that less well-off schools were subsidising wealthier schools.
"But these really are matters for Catholic education to explain to its parents, to its constituent bodies."
Catholic school funding will increase by $1.2 billion over the next four years, he said.
The data provided to Fairfax Media shows high-SES NSW Catholic primary schools in Coogee, Annandale and Woollahra were funded above their allocation, while low-SES schools in Tenterfield, Walgett and Campsie were significantly under-funded.
Low-income Victorian Catholic schools in Tallangatta and Heathcote were funded significantly below their allocation, while high-SES schools in Caulfield and Ivanhoe East were overfunded.
Danielle Cronin, acting executive director of the National Catholic Education Commission, said the Catholic sector's method for redistributing funding allows "low-fee Catholic schools to be present in communities all across the country".
"Our education experts are better able to look at the needs of a community than a blunt instrument like a funding formula entered into a spreadsheet," she said.
"Our colleagues know if there are particular needs that don't show up in funding calculations.
"They know far better than the flawed SES methodology what the real capacity of parents and families to pay fees is in an individual community."
At the weekend, the National Catholic Education Commission released estimates of fees increases of up to $6000 at some schools and was reported to be planning a "mining tax-style campaign" against the government.
The campaign is expected to focus on grassroots efforts such as letters from principals to parents rather than a massive advertising spend.
Martin Hanscamp, head of the Australian Association of Christian Schools, said he understood the Catholic sector was upset about losing its generous funding arrangements but said it should adopt a less "self-interested" stance.
"In our reactions, it is tempting to focus on what we might lose and to react with a 'don't touch what's mine' response," he said.
"When we do this, however, we lose sight of what is valuable for us all, for all sectors, for all Australian schools.
"We need to give this legislation our support because of the opportunity it provides for a massive breakthrough in the rolling, unstable, divisive approach to funding that we have had for so long."
Mr Hanscamp represents 126 Christian schools, some of which would have their funding cut under the government's new model.
He said that while it was not as generous as Labor's arrangements, the government had devised a "fair, long-term affordable model that can bring stability to this area of worn-out confusion and debate".
