A number of Border schools were identified in the Australian National Audit Office report, with some receiving twice as much federal funding than what they were allocated, while some others got between 30 and 73 per cent less than what they were allocated. 

For example, Wangaratta’s Cathedral College was allocated $4,617,145 in 2015 under the Australian Education Act (2013), but received $8,948,642.

St John’s Primary in Jindera, St Paul’s in Henty and St Michael’s in Tallangatta were among the schools to have a decrease in funding of at least 30 per cent or more. 

St Paul’s in Walla was given twice as much finding compared to what had been allocated to them by the federal government, while St Joseph’s in Finley were also advantaged by surplus funds.

The individual school funding is assessed on a needs basis, but the actual payments are often distributed through a central body, rather than given directly to the schools.

The Audit Office found those authorities had re-distributed the funding as they saw fit, short-changing some schools and giving extra money to others.

Only nine of 33 education authorities published details of how they divided government money among their schools.

The report, released on Wednesday, found the education department did not have “sufficiently robust arrangements” to ensure needs-based funding complied with the law.

"Overall, the arrangements established by the department have not delivered the level of transparency and accountability envisaged,” the report read.

Eleven per cent of schools funded through a central body received at least 10 per cent more funding than what they were allocated in 2015.

A further 12 per cent of schools received at least 10 per cent less than their allocation.

The National Catholic Education Commission said the funding formula has “serious flaws.”