Victorian independent schools have been accused of "gaming the system" to almost double their federal funding for students with a disability.

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".