Thousands of students could discover the fees at the universities to which they have applied are to change, just weeks before the application deadline.
The Office for Fair Access is expected to announce later how many of England's universities have sought fees changes for 2012.
Universities blame delays in planned changes to higher education.
Ministers said it had been made clear any changes should not disadvantage students who had already applied.
Maximum tuition fees will rise to as much as £9,000 a year next autumn.
Universities were required to submit their plans for higher charges, bursaries and fee-waivers for certain groups of students back in April. These were then assessed by the fair access regulator, Offa.
But because of delays to the government's planned changes to higher education this was at least two months before the government published its proposals in a White Paper.
These included allowing universities charging less than £7,500 a year in fees to expand.
This was widely seen as a last-minute measure to bring the overall cost of higher fees down for the government after it became clear that more universities than expected were planning to charge maximum fees.
Nicola Dandridge, head of umbrella group Universities UK, said the timing of government announcements on policy changes was frustrating.
She added: "This has come about because universities were asked to set their 2012-13 fee levels and financial support by April this year, before the details of student number controls had been decided.
"The delayed publication in June of the government's White Paper then shifted the goal posts [of student number controls].
"Some universities will now have to reduce their net fee levels to ensure they can offer opportunities to students who want to study with them.
"Any universities making revisions to their access agreements will be contacting all students who have already applied to let them know of any changes to their financial support package."
She added that universities that revised their 2012-13 access agreements might be simply changing their package of financial support for students - and it was not just a question of reducing their fee levels.
As many as 28 universities could have sought to bring their original fees down or offer more generous bursaries and fee-waivers.
It comes just nine weeks before the 15 January deadline for university applications, but nearly 70,000 students have already applied for courses for 2012.
The vice-president of the National Union of Students, Toni Pearce, said the government's incoherent changes to higher education funding continued to wreak havoc and chaos on students and universities.
She claimed ministers had realised that they had failed to do their sums properly, adding: "Tens of thousands of applicants now face an anxious wait at an already stressful time.
"Students looking to assess and compare what support will be available to them will be facing weeks of uncertainty, and many will find that vital bursaries have been replaced with tokenistic fee-waivers."
A Department for Business, Innovation and Skills spokesman said: "We are putting students at the heart of the system, with a diverse range of providers offering high-quality teaching.
"It is up to individual institutions to decide what they charge students, subject to having an access agreement in place if they wish to charge more than £6,000.
"The Director of Fair Access has made it clear that students need to come first and anyone who has already applied should not be disadvantaged by any changes. Institutions are expected to contact any affected students to explain any changes."