The National Union of Students has been criticised for advising student leaders to "engage" with university leaders rather than just campaign for lower fees.
The advice is in a memo which describes the new system as "relatively progressive".
University tuition fees are set to rise to a maximum of £9,000 in England.
The NUS says it is still opposed to the fee rise but unions should try to "secure clarity and value from fees".
It has already been accused of being "soft" in its opposition to higher fees, due to come in in England in 2012.
Fees are currently set at £3,290 a year.
Nationally, the NUS has opposed any increase in fees and calls for a graduate tax instead, but it is advising union leaders at individual universities to be pragmatic - and to make sure they are involved in university-level discussions about where fees should be set.
Universities are currently debating fee levels and student leaders are members of university governing bodies so can be involved in the talks.
Imperial College London has become the first university officially to set its fees at the maximum level allowed - £9,000 a year.
Oxford and Cambridge appear to be moving close to doing the same.
The memo, which is on an NUS website, gives a detailed breakdown of the system being brought in, including details of the loans and grants available and assesses the way universities might be thinking as they come to set fees.
It says: "Recognising that simply campaigning for a low fee might not generate the results you require (especially inside the Russell and 1994 group), NUS would recommend you engage in detailed discussions with councils and execs to discuss the issues at stake before engaging in detailed discussions."
This is understood to refer to the idea that universities might suffer and have to cut courses if they do not raise enough money from fees.
The memo describes the new system as "relatively progressive".
It says: "The loan gets written off after 30 years (currently 25) - the vastly increased numbers of graduates that will never pay the loan off are in fact what makes the system relatively progressive (though the richest will never take out a loan and and higher earners will pay off early, avoiding interest)."
On the cuts facing the university sector, it says: "Much has been made of the government's 80% cuts to teaching budgets; of course, while that is true, there has not been an 80% cut to the overall universities budget - in fact the subsidy has been moved in to this state-backed loan-based voucher scheme.
"Overall, the government will put in about 40% less, with the rest assumed to be being made up by larger contributions from richer graduates."
President of Cambridge University Students' Union, Rahul Mansigani, said: "It is disappointing that anyone views as progressive a scheme that the NUS, Cambridge University Student Union and students up and down the country campaigned against.
"The new fee system shifts the funding burden from the government into vast debts for students, and is a cynical and damaging attack on our university system."
Second year Exeter student Jamie Brown told the Times the NUS needed to "make its position clear".
"The most disappointing thing is that the NUS is not being honest," he said.
The NUS rejects that claim and insists there has been no change in its position - it continues to oppose the fee rise.
NUS president Aaron Porter said: "The system is baffling, chaotic and short-sighted - so our advice to students' unions is to secure the maximum clarity and value from the fees their university will set.
"It is a fact accepted by all involved, including university heads, that there will be an 80% cut to direct government teaching grants, enabled by a huge 40% cut to government funding of universities overall and by pushing the subsidy that's left into writing off loans that students will still be saddled with after 30 years."