Lauriston Girls School is one of the big winners, and stands to gain almost $3.2 million of extra federal funding between 2018 and 2027, according to an analysis of previously secret data that will inform the Turnbull government's new Gonski 2.0 school funding model.

Bialik is set to receive an extra $2.7 million, St Catherine's $1 million and Christ Church Grammar $492,000.

The dramatic change in estimated funding has largely been driven by these schools reporting "significantly higher" numbers of students with a disability, according to the federal Education Department.

A confidential report obtained by Fairfax Media shows Victorian independent schools reported that 26 per cent of their students had a disability in 2016.

This compares with 17 per cent of Victorian state school students and 13 per cent of Catholic school students and is the highest figure in any school sector in the country.

But not every student qualified for the funding. The report revealed that 12.7 per cent of Victorian independent school students were eligible for disability funding. This compared with 10.6 per cent of Victorian state school students and 8.9 per cent of Catholic school students.

The report prepared for the Education Council details the 2016 results of Nationally Consistent Collection of Data on School Students with Disability – information collected by schools which will help determine school funding from next year.

These figures feed into the schooling resource standard, which measures how much government funding schools are entitled to.

Australian Education Union federal president Correna Haythorpe said the data – which the union obtained via freedom of information – revealed "alarming discrepancies".

"In 2017, schools considered to be funded above the schooling resource standard are suddenly projected to sit significantly below it in 2018, when the need of their students cannot possibly have changed to such a drastic degree," she said.

Lauriston principal Susan Just said the data the school had collected on students with a disability was confidential. "We hope that all students with individual needs will be recognised in the school's funding allocation," she said.

"It is oversimplifying the process to say Lauriston has gone from overfunded to underfunded. The new needs-based funding model is different to the old system, and the criteria have changed."

She said enrolments fluctuated and the needs of students changed, so it was misleading to predict how much funding the school would receive in the future.

In 2017, Lauriston was considered overfunded because it received 130 per cent of its funding entitlement from the Commonwealth and state government.

More than 102 per cent of this came from the Commonwealth, but this has been revised down to 49.6 per cent for next year.

Under the new Gonski school funding model, the federal government must provide 80 per cent of needs-based funding to private schools, which will lead to significant funding increases for these schools. State governments are expected to make up the remaining 20 per cent.

The opposite has occurred at non-government schools considered less needy. They will therefore receive less generous funding increases under Gonski 2.0 – Haileybury moved from 78.7 to 85.8 per cent of its funding entitlement, Penleigh and Essendon Grammar increased from 80.06 to 82.9 per cent and the Catholic education commission of Victoria increased from 75.02 to 79.8 per cent.

An Education Department spokesman said the figures were not comparable and had changed to reflect current financial settings and student data.

"The main driver of the differences in estimated funding for these schools is that they reported significantly higher counts of students with disability in the 2016 NCCD [disability data] compared to the less detailed census data," he said.

He said payments for 2018 would be based on more recent disability data, which is being finalised. The new model includes four categories of disability (physical, cognitive, sensory and social/emotional) and students are funded accorded to the level of support that they receive.

Public education lobby group Save Our Schools, which is run by former Productivity Commission economist Trevor Cobbold, analysed the data and said it showed "unjustifiable increases" in Commonwealth funding for several of Melbourne's "most elite schools".

"Some schools with more than 75 per cent or more of their students from the top socio-educational advantage quarter will get increases of between $2.6 million and $3.2 million," Mr Cobbold said.

Independent Schools Victoria chief executive Michelle Green said previous methods for assessing the eligibility of funding for students with a disability were narrow.

"It is misleading to compare figures on students with disability and any related allocation of government funding, when methods of assessing them have changed from one system to another," she said.

"In many cases, assessing a student as having a disability – asthma, for example – does not entail additional government funding."

She said the organisation was committed to ensuring that the data was collected consistently across sectors.

Federal Education Minister Simon Birmingham said the new funding model would deliver fairer, needs-based funding and was supported by dozens of independent experts.

He said funding for state schools would grow by an average of 6.4 per cent per student, every year, over the next four years, compared with 4.2 per cent growth for non-government schools.

"Our plan ensures that within six years all schools receiving less than their Commonwealth share of the schooling resource standard will be brought up to that level and all notionally overfunded schools will be brought down to the SRS within a decade, unlike the 150 years it would have taken if we'd let Labor's arrangements continue," he said.

The Gonski 2.0 funding changes passed Parliament in June.