The Education Department data, released to Fairfax Media, revealed Holy Rosary School in Heathcote was among those funded significantly below their federal government funding allocation.

The government funds Catholic schools on a needs basis but distributes the money to state and territory education commissions in a lump sum, which they distribute among schools as they see fit.

The most socially disadvantaged Catholic school in Victoria, St Thomas Aquinas in Norlane, received 15 per cent less than its federal government funding allocation in 2015, while St Columba's School in the affluent Melbourne suburb of Elwood received 15 per cent more funding than its allocation. 

Holy Rosary received $10,935 in federal funding per student in 2015, down from $13,589 the previous year, according to the My School website.

The revelations come after Sandhurst Diocese Catholic education director Paul Desmond spoke out against the government’s “Gonski 2.0” funding package earlier this month, saying it had damaged the relationship with the Catholic sector.

“I believe the independent sector is well looked after in this funding scheme [but] I think to fund the Catholic sector at a lower rate beggars belief,” he said at the time.

“The goodwill that has always existed with the Commonwealth government has taken a hit. However, we will find a way of working together again for the good of the students in our care.”

Education Minister Simon Birmingham said Catholic school funding would increase by $1.2 billion over the next four years.

 "I think people would be very concerned if they thought that less well-off schools were subsidising wealthier schools,” he said.

"But these really are matters for Catholic education to explain to its parents."

Mr Desmond was contacted for comment.

With – The Age