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An analysis of the latest figures on the MySchool website shows 1115 private schools in Australia are receiving more income per student than the average state school, through school fees, parent donations and government funding.
These schools received $2.1 billion in Commonwealth government funding in 2013, the equivalent of nearly one third of the final two years of the Gonski funding deal.
It comes as Fairfax Media revealed that federal Education Minister Simon Birmingham would ditch the final two years of the Gonski deal in favour of negotiating fresh funding deals with the states from 2018.
Mr Birmingham warned that the government did not have a "limitless" amount of money to spend on schools.
Trevor Cobbold, who is a former Productivity Commission economist and public school advocate, crunched the MySchool figures.
He said too much Commonwealth funding was flowing to schools that did not need it. This was due to an "incredibly favourable" funding arrangement for private schools under the previous Howard government, which has been folded into new school funding models for the non-government school sector, he said.
"We have continued to fund privilege rather than disadvantage in education," said Mr Cobbold, who is the Save Our Schools (SOS) spokesman.
"It's a straight choice. Do you fund wealthy private schools at the expense of disadvantaged schools, or do you turn some of that funding around to support disadvantaged students in the public and private sector?
"The government over the last 15 years has chosen not to do the latter ... that means that students from disadvantaged families will continue to be disadvantaged through their lives. They will face high unemployment, low incomes, and not participate fully in the workforce and the economy. It's not just a matter of social justice, it's a matter of economic growth."
A Productivity Commission report revealed earlier this year that Victorian state schools students each get almost $2000 less than the national average.
The report also showed that funding for Victorian state schools fell over the 2012-13 period, while funding for students in independent and Catholic schools rose.
State schools are largely funded by the state government and educate the bulk of the state's most disadvantaged.
Catholic Education Office executive director Stephen Elder said Mr Cobbold's analysis focused exclusively on socioeconomic advantage, which did not apply to all private schools.
"'Socioeconomic advantage is not the sole domain of private schools. As we pointed out during the recent Bracks review of government school funding in Victoria, there are high concentrations of advantaged students in a number of government-run schools."
Mr Birmingham said the Turnbull government would spend a "record" $69 billion on all schools over four years from 2014 to 2019, and the government was committed to funding that "looks beyond just a two-year horizon".
"The Turnbull government knows that funding is important but that what you do with it matters even more. The government's discussions on future funding will not just be about how more money is spent but will seek to ensure we lift education outcomes too."
The six-year Gonski school funding deal was designed to support students based on need.
The Independent Schools Victoria was not available for comment.