In a rare moment of unity, the Australian Education Union and Catholic Education Melbourne have joined calls for an independent review of new disability data tied to the Gonski 2.0 school funding model.

Funding was previously based on medical assessment, but under the new system it is based on teachers' assessments of students' needs.

The union's federal president Correna Haythorpe called for an independent audit into "what appears to be a further gold-plating of the private system at the expense of children in public schools".

More than half the total funding increases for Australian students with a disability are set to go to Victorian independent schools in 2018, she said.

Catholic Education Melbourne executive director Stephen Elder described the new disability data as "dodgy".

"Education Minister Simon Birmingham is letting wealthy independent schools - the biggest backers of his funding policies - game the system," he said.

He said public funding for students with a disability would now be steered towards schools with "the most creative data collection practices" and away from students who need it.

"No one believes the new disability data is credible," Mr Elder said.

"It inherently favours wealthy schools... [they] can afford to make more adjustments for their students - and they also have the staff to complete all the paperwork."

Federal Education Department figures, obtained by the union under Freedom of Information, show that disability loadings for Victorian independent schools will increase from $63.7 million in 2017 to $123.3 million next year. They will then grow to $222.2 million by 2027.

But Catholic schools stand to lose $16 million next year before their disability funding increases to $228.3 million over the next decade. Disability funding to Victorian government schools will increase by 11 per cent next year, growing to $304.2 million.

Independent Schools Victoria chief executive Michelle Green said that the figures did not lend themselves to "easy point scoring".

"These figures reflect a recognition of a need that was previously not recognised," she said.

"They also reflect a redistribution of funding within a school's entitlement, to increase the funding for students with disability at the expense of other loadings that the school might receive."

She said funding for students with a disability was not biased towards any sector.

In 2016, Victorian independent schools reported that 26 per cent of their students had a disability, according to a confidential report obtained by Fairfax Media.

This was the highest figure in any school sector in the country. In comparison, Victorian state schools reported that 17 per cent of their students had a disability and Catholic schools reported 13 per cent.

Federal Education Minister Simon Birmingham said further work was needed to improve the quality and consistency of the data.

"This new system sets clear definitions and we're implementing a range of checks for funding for students with disability to ensure funding gets to the students that need it most," he said.

He said the government was investing $20 million to improve the quality of the data and it would be independently verified.

"Under our plan funding for students with disability will grow from $1.5 billion this year to an estimated $2.7 billion. Funding for students with disability in Victorian government schools will increase by an estimated 108.2 per cent and by 97 per cent for non-government school students."

He said the data was based on projections and it would be updated to reflect actual enrolments in 2018.