Students appear to be more ready to complain
The university adjudicator for England and Wales received 900 complaints from students in 2008 - a rise of 23% on 2007 - but just 7% were upheld.
Disputes over postgraduate courses and allegations of plagiarism pushed up the total, the Office of the Independent Adjudicator for Higher Education said.
The adjudicator said the rise reflected a "cultural change" with fee-paying students wanting more value for money.
Universities said the figure should be seen in the context of 1.9m students.
There have been claims that students paying tuition fees were becoming more consumerist in their attitudes, with higher expectations of getting value for money from their courses.
Adjudicator Rob Behrens says that such a consumer awareness among students is "not necessarily a bad thing".
The 23% rise in complaints in 2008 follows a 25% increase in 2007 compared with 2006.
But only 7% of the complaints were upheld - with many falling outside the adjudicator's remit.
The office cannot address some of the most contentious areas of higher education - such as admissions and academic judgments such as the awarding of degree grades.
It considers only complaints which have failed to be resolved by the disputes procedures within universities.
There was a disproportionately high number of international students among complainants - and Mr Behrens says this reflects a greater assertiveness among those paying higher fees.
But it also overlaps with the increase in disputes over plagiarism - and he says there were questions about different cultural attitudes towards what constitutes plagiarism.
Mr Behrens says this emphasises that universities should make clear how plagiarism will be interpreted, before any ambiguities can arise.
When there are disputes over universities' handling of plagiarism accusations the report says that "practice is variable".
It says in a small number of these cases, there were "conflicts of interest" in the handling of complaints.
Postgraduate courses also "feature prominently in our case files", says the report.
The report found cases where there had been "a clear reluctance to give timely feedback to underperforming postgraduate students".
"This creates false expectations of successful outcomes from thesis submission and is something that could be avoided."
Business students were the most likely to have pursued a complaint.
The rise in complaints is against a background in which students are seen to have much greater expectations of receiving value for their tuition fees.
Earlier this year, students at Manchester Metropolitan University set up a text service for disgruntled students who were kept waiting for their lectures.
Diana Warwick, head of the university vice-chancellors' representative body, Universities UK, said the rise in complaints reflected "the increased awareness of this complaints procedure".
But she said that the 900 complaints handled by the adjudicator should be seen in the context of 1.9 million students.
And a spokeswoman for England's Department for Innovation, Universities and Skills said: "According to the latest student survey, 80% of students are satisfied overall with the quality of their university experience.
"The OIA provides an important service for the small percentage of students that have outstanding issues."
But the National Union of Students said that there were still too many delays within universities in addressing complaints.
"Many universities need to work much harder to make their complaints procedures more efficient and transparent."