Elite universities with poor records of enrolling disadvantaged students would be the big winners under the federal government's new Commonwealth scholarship scheme, according to new modelling.

Regional and suburban universities – which typically enrol more students from poor backgrounds – may have only 20 per cent of the funds to spend on scholarships for disadvantaged students as their elite counterparts, according to the National Tertiary Education Union modelling.

The federal government last week introduced legislation into Parliament that, if passed, would allow universities to set their own fees and reduce Commonwealth course funding by 20 per cent.

Universities would be required to spend $1 of every $5 in increased fees on equity scholarships for disadvantaged students.

The union's modelling found that a regional university with 30 per cent of disadvantaged students would have $1733 to spend on scholarships for each such student under a deregulated fee system.