More than a fifth of England's universities have applied to change their fee packages, just weeks before the application deadline.
The Office for Fair Access said 27 of England's universities had sought to lower fees to make use of new measures that could allow them to expand.
Universities blame the late announcement of these measures by the government.
Ministers say changes should not disadvantage any student.
But the National Unions of Students said tens of thousands of students now faced weeks of uncertainty because of the changes.
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.
This was before the government published its proposals in the Higher Education White Paper, which was delayed by several months.
The plans included allowing universities charging less than £7,500 a year in fees to expand by bidding for 20,000 degree places.
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.
Offa said it had received applications from 27 institutions wishing to reduce their average fees to £7,500 or below in order to bid for the 20,000 places set aside for this purpose.
It also said it had received new access agreements from seven publicly funded further education institutions wishing to bid for some of these places.
The watchdog says it will assess the revised agreements and inform universities and colleges of its decisions by November 30.
In the meantime, institutions must contact applicants affected by the changes and let them know. Would-be students will then have the chance to reconsider their options.
Offa also said it would consider any further changes from universities still wishing to change their access agreements.
Nicola Dandridge, head of umbrella group Universities UK, said: "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]."
Vice-chancellor of West London University Professor Peter John said the university had decided to lower its fees slightly from £7,498 to £7,400 after the mechanism for calculating average fees was changed.
This had pushed them over the level at which they could bid for extra students on the basis of offering a cheaper course.
He also said the fact that a number of policy changes came quite late had added "much uncertainty to applications in an already uncertain environment".
"The government haven't helped in their message, they have not been clear and there is a lot of concern and anxiety - some students still believe they are going to pay fees up front," he added.
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. Applications from UK students are down year-on-year by 12%.
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.
"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."
The general secretary of the UCU lecturers' union, Sally Hunt, said: "Leaving universities and students to scramble around trying to save a few quid here and there is no way to run a world-class university sector.
"The government's decision to move the goalposts on fee levels after it got its sums wrong exposes the mess it has made of university funding."
Labour's shadow higher education minister Shabana Mahmood said: "It is unbelievable that students have had to apply for courses before knowing how much they will pay in fees.
"The government's rushed and haphazard cuts to higher education budgets go too far, too fast, with universities unable to plan ahead and frustrated students without the full information to help them apply."