Urging the government to make good on its promise to "put students in the driving seat", Liam Burns said university governance reform was needed to give students a greater say on strategic documents, such as access agreements and student charters.
He called for universities to give at least a quarter of their council seats to students, saying they should require student consent when signing off key documents, including long-term development plans.
Institutions seeking to charge tuition fees above £6,000 a year currently need approval from the Office for Fair Access - an independent but state-funded body - before setting charges for 2012.
"If students are at the heart of the system, it has to be put into effect," Mr Burns told an audience at the Enhancing the Student Experience conference in London last week.
"We should not have a state- controlled body as our champion. It wouldn't be a blanket veto [on fee levels], but there should be a way for students to say, 'We are full partners in this and we want change.'"
Student charters, which outline student rights and responsibilities, should also be mutually agreed by staff and unions, Mr Burns argued, because they were being watered down by lawyers afraid of legal recourse if rights were too clearly defined.
"They are being sent off to the lawyers and come back with all the responsibilities remaining, but the rights ripped out of the document.
"Students will not participate in a process if it is to be thrown back in their faces."
Without more student influence on decision-making, any claims that government plans "empower" students were merely rhetoric because individuals had little sway over their institutions, he added.
He also branded fee waivers a "bare-faced con", and called the National Scholarship Programme, which will be worth £150 million by 2015, a "disaster".
Addressing those institutions that advocated fee waivers over upfront bursaries, he said: "I understand you are in a straitjacket, but you are failing students. To subsidise the Treasury rather than students is a scandal."
Key Information Sets, which will provide students with standardised data on contact hours, graduate employment success and fee levels from 2012, were also criticised during a panel discussion at the conference.
Paul Greatrix, registrar at the University of Nottingham, said that compiling KIS data would be a "very expensive" burden and would have little impact on students' choices.
"There is a danger of overwhelming students with data," added Carolyn Fowler, registrar and secretary at Durham University. "Data on a website only say so much - you cannot beat taster days and visits to a university."