The changes reflect new data – which the Catholic sector has previously described as "dodgy" – that determines funding under the Turnbull government's Gonski 2.0 model.

Funding for students with a disability was previously based on medical assessments, but is now based on teachers' assessments of students' needs.

New federal Education Department figures show that Commonwealth disability loadings for Victorian Catholic schools will increase by 26 per cent, to $188 million in 2018.

Disability loadings for Victorian state schools will grow incrementally, by 5.6 per cent, to $171.7 million, while those for independent schools will dip 4.5 per cent to $117.8 million.

Victorian state schools – which educate 71.3 per cent of funded students with a disability according to the Productivity Commission – were previously set to receive the largest share of Commonwealth disability funding.

Catholic schools were initially projected to lose disability funding next year.

The Australian Education Union repeated its calls for an independent inquiry into the data.

"Government schools educate the vast majority of students with disability and yet in Victoria they won't even get the largest share of disability funding from the federal government," the union's federal president Correna Haythorpe said.

The changes are due to updated data collected by schools as part of the Nationally Consistent Collection of Data on School Students with Disability.

This data – which is based on a much broader definition of disability – will help determine school funding from next year.

Catholic Education Commission of Victoria executive director Stephen Elder said the data should not be used to allocate funding.

"Less than 12 months ago Education Minister Simon Birmingham declared that the NCCD 'fails a basic credibility test'," he said.

But Mr Elder said he would ensure every student who was eligible for funding was included in the data.

He said Catholic schools received more Commonwealth funding for students with a disability because they educated more students than the independent sector.

He pointed out that the Commonwealth government is the major public funder of non-government schools while state governments are the major funders of state schools.

Large fluctuations in the data have led to a dramatic drop in overall estimated funding for some independent schools.

For instance, Commonwealth funding at Lauriston Girls' School under the Gonski 2.0 funding model has been revised down to a 21 per cent increase over the next decade, compared to the 128 per cent increase initially projected.

Shelford Girls' Grammar is now set to receive a 39 per cent increase compared to the 113 per cent increase initially earmarked for the school.

An Education Department spokesman said these changes were "largely driven by changes in the number and level of adjustments of students with disability".

He said that the department had worked with schools who reported apparently irregular results to resolve errors, but would not say which schools had been contacted.

Independent Schools Victoria chief executive Michelle Green said schools had worked hard to improve the quality and consistency of the data.

"As a result of this work, we understand there is a significant difference between 2016 and 2017 data for Victorian schools – not so much in number of students identified with disability, but more around the levels of adjustment being provided by schools to meet the needs of individual students," she said.

She said the number of students with disability could change from year to year, as could their needs. Ms Green said the old data collection was based on a narrow definition of disability and the new model was superior.

Federal Education Minister Simon Birmingham said the new model would support an additional 273,224 students and deliver an extra $1.3 billion.

"It's galling to see some special interest groups attempt to undermine what has been a bi-partisan policy just because the results don't suit one particular agenda or another," he said.

He said funding for students with disability would grow from $1.5 billion this year to an estimated $2.8 billion by 2027.

"Funding for students with disability in government schools will increase by an estimated 98 per cent and by 73 per cent for non-government school students, reflecting the needs-based funding model we're implementing," he said.