The university sector will be waiting to hear its funding future, with a number of recommendations to reduce the role of public money.

Students will pay more, governments less and universities will be able to charge what they want, if all the recommendations from the Commission of Audit are taken up.

The notion to deregulate university fees has been raised before, and is present in the Commission’s report. The rationale is that deregulation would lead to more competition, better quality and more innovation.

There are no clear facts or figures to back this up, prompting the call for a full report into deregulation specifically.

On the research side, the report suggests abolishing the Industry Innovation Precincts Program, Collaborative Research Networks and a number of other industry/university linking schemes.

It recommends “streamlining” both the NHMRC and ARC grants processes, running grants for longer periods, changing postgraduate scholarship arrangements and reducing research “block grants” for data-collection, grant registrars and other supporting activities.

For the government auditors, it appears that students are not paying enough to attend tertiary institutions.

The audit report says that students currently pay about 41% of their total tuition costs, with the rest coming from Commonwealth subsidies.

The auditors propose lifting the student average to 55% and reducing Commonwealth input to 45%.

In 2013, the Commonwealth put $6.1 billion into subsidising universities directly, with students spending $4.2 billion primarily through HELP loans.

Figures suggest that if students had to provide 14% more of the $10.3 billion spent in 2013, the government could save $1.4 billion.

But given that most of that figure would be HELP debt, there is speculation as to whether the savings would be tangible at all.

To get more out of HELP loans, the audit recommends lowering the threshold at which graduates repay their loans.

Repayments are currently triggered at $51,300 a year. The report proposes starting repayments at the minimum wage, currently $33,250.

The argument has been raised that this does not match financial assistance triggered at higher thresholds, such as the Family Tax Benefit Part A, which applies to family incomes over $48,800.

Some say taking HELP repayments form people on minimum wage with no other assistance would unfairly slug graduates.

The Commission also recommends “streamlining” the various HELP schemes to iron out anomalies between versions of the program.

Currently there is a 25% loan fee on bachelor level FEE-HELP plans for those studying at non-public universities, but this is not applied to HECS-HELP loans or to FEE-HELP loans for postgraduates.

Auditors recommend setting up a flat interest rate across HELP loans, which would reflect the full cost of the multi-billion-dollar HELP loans and associated debts.

A recent report from the Grattan Institute showed the pile of HELP debt is now approaching $13 billion.