Labor says it is the first sign of an arrogant Government.
Education Minister Brendan Nelson says he will use the Government's Senate majority from July 1 to pass changes previously held up in the Upper House.
They include an end to compulsory student unionism and a plan to extend the use of Australian Workplace Relations agreements.
Dr Nelson also wants the Commonwealth to take over control of universities from the states.
He says the current arrangement is ridiculous.
"Because they've got different laws governing them in different states," he said.
Labor's Jenny Macklin says it is a sign of an arrogant government.
"Neither John Howard nor Brendan Nelson made any mention of these plans during the election campaign," she said.
The National Tertiary Education Union president Caroline Allport says the plan will only promote greater discord and uncertainty in the sector.
"This interference by the Government will promote dissension," she said.
"There's likely to be industrial action there, and of course we will not rule out any further industrial action such as national strike action."
University vice-chancellors have also criticised the plans, saying it would give the government too much power over the sector.
Australian Vice-Chancellor's Committee chief executive John Mullarvey says the move is unlikely to get any support from the body.
"Vice-chancellors won't be enthusiastic about that idea because it would put the power to determine future directions of universities, both in funding and in mission, in the hands of one minister, irrespective of which persuasion," he said.
University of Western Australia vice-chancellor Alan Robson says Dr Nelson should spend more time ensuring universities are adequately funded.
Professor Robson says the Federal Government is yet to complete a review into indexation of grants to universities.
"If we are really going to address the quality of what goes on within universities the biggest thing is to increase funding per student," he said.
"I think that's a much more important issue for universities than the issues proposed by Dr Nelson.
"These other things are sideshows to the main game."
States
Queensland Premier Peter Beattie says the Federal Government will have a fight on its hands if it tries to take total control of higher education away from the states.
Mr Beattie says Dr Nelson's plan would be a step backwards.
"[The] Federal Government has done very little," he said.
"Now they are failing our universities, failing Queensland when it comes to university places, and it's not good enough.
"If they think we're going to back off over fighting for a better go for universities, they're wrong."
Mr Beattie says the Federal Government can not be trusted to take full control over universities.
"This is where control of the Senate has gone to their head," he said.
"I mean they need some checks and balances - they're now out of control."
South Australia's Further Education Minister Steph Key says she will be interested to hear Dr Nelson on the issue of banning compulsory student unionism.
"I'll just remind him that some of his colleagues came up through the student movement and Peter Costello and Tony Abbot are two that come to mind when I was at uni and when he was at uni," Ms Key said.
"So I'll be interested to see what he says about that."
Western Australian Education Minister Alan Carpenter has also dismissed the proposals.
He says the reforms are designed to crush university unions and seize legislative control of universities from the states.
"Our State Government would be very, very reluctant to embrace the transfer of that legislative authority to the Commonwealth under the present circumstances, with the present agenda," he said.
The Victorian Government says there are many reasons why it might be reluctant to agree to the Federal Government's plan to overhaul the university sector.
A Victorian Government spokeswoman says while the state is willing to consider all proposals, it might be reluctant to sign anything given the Commonwealth's record of neglect of the higher education system in recent years.
She also says there are some universities in Victoria that play a particular role within the state, including Victoria University of Technology which has a charter to serve Melbourne's west.
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