The tertiary education union has accused Education Minister Christopher Pyne of undermining ministerial responsibility by introducing laws he knows will hurt students and universities.
The government moved on Thursday to legislate $1.1 billion worth of cuts to universities that Labor announced in April.
The bill imposes a two-year efficiency dividend on universities, saving the government $900 million, and gets rid of discounts for upfront and early repayments of HECS-HELP debts, garnering another $237 million.
Mr Pyne said the government also intended to legislate the $1.2 billion measure to convert student start-up scholarships to loans.
"These are Labor's cuts," he told parliament, painting the coalition as "the true friend" of universities and students.
The coalition has dumped only one of Labor's planned cutting measures: a cap on the amount of tax deductions people could claim for work-related education expenses.
National Tertiary Education Union president Jeannie Rea said it wasn't good enough to blame the previous government for the cuts.
"I find it extraordinary that the minister would introduce legislation into parliament which he openly acknowledges ... will be damaging to our universities and their students," she said.
"This undermines my understanding of ministerial responsibility, if ministers blithely get away with policies which they know will damage institutions for which they have responsibility."
The higher-education sector campaigned strongly against the cuts when they were announced in April and again in the May budget.
The Australian Greens will vote against the legislation and called on Labor to help them block it in the Senate.
Universities Australia chief executive Belinda Robinson said the sector was disappointed when the previous government proposed stripping $3.8 billion from higher education and students - and it remains concerned at the widespread impact of the cuts on teaching and research programs.
"These have been at least partly offset by the government's very welcome decision not to go ahead with the $2000 cap on tax deductions for self-education expenses and should also be seen in the context of positive commitments by the government on reducing red tape and rebuilding international education," she said in a statement.
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