University students will pay an average of $50,000 for a three-year degree by the middle of the next decade should the federal government succeed in deregulating fees, analysis by the independent Parliamentary Budget Office shows.

The fee estimate is included in a PBO report revealing a huge blowout in the cost of the government's Higher Education Loan Program (previously known as HECS).

In the 2014 budget, the Coalition announced that it would cut funding to university courses by 20 per cent but allow tertiary institutions to set their own course fees.

The changes were torpedoed in the Senate and last October the newly appointed Education Minister, Simon Birmingham, delayed university reforms until 2017.