The federal government has no plans to directly fund individual Catholic schools despite data showing needy schools are being short-changed up to $1.5 million a year to keep fees low in wealthy areas.
Education Minister Simon Birmingham said the government would continue to allow state and territory education commissions to distribute, as they see fit, the lump sum they receive from Canberra.
"We expect them to abide by the needs-based funding principles," he told ABC radio ahead of a parliamentary debate on government legislation on Tuesday.
Senator Birmingham said across the country the Catholic education sector would receive real growth - $1.2 billion - over the next four years.
Government data provided to Fairfax Media shows NSW Catholic primary schools in wealthier suburbs like 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.
Senator Birmingham said it was up to Catholic education authorities to explain how they distribute federal funds.
"They will need to be answerable ... to their parents, teachers, school communities about how they're doing so and whether that is fair and appropriate," he said.
The National Catholic Education Commission has released estimates of fee increases of up to $6000 at some schools and was reported to be planning a "mining tax-style campaign" against the government.
At least one Catholic school principal has taken issue with the commission's warning.
Madonna Sleba, from Mater Dei Catholic Primary School in Brisbane, has written to parents telling them "our fees will not be increasing in anything like the way suggested by that article".
Opposition education spokesman Tanya Plibersek predicts the government has a "real mess" on its hands it fails to heed the concerns of principals, teachers and parents.
"We will be opposing these cuts every day in every possible way," she told ABC TV.
Senator Birmingham insisted all non-government schools should enjoy a single funding model and profile.
"We are not about to entertain ideas that would go back to different deals or creating a system that advantages one type of non-government sector over another or one state over another," he said.
"Australians are sick and tired of that."
