Students have become more willing to issue formal complaints about their treatment at the hands of universities since the imposition of £9,000 annual tuition fees, the higher education watchdog has revealed in its annual report.

The Office of the Independent Adjudicator (OIA) – which reviews complaints from students in England and Wales – said that appeals jumped by 20% between 2011 and 2012, the first year of the new, higher fee level.

"The expectation is that higher tuition fees will lead to more complaints. The increase will undoubtedly provide major challenges for universities, students' unions and the OIA," Ram Gidoomal, the chair of the OIA's directors, wrote in the organisation's annual report.

While the bulk of appeals were turned down, the adjudicator decided nearly one in five appeals in favour of the complainant. Compensation payments totalled £190,000.

In one case, a group of postgraduates complained to the OIA that their university had "misrepresented important facts about an MA course," and that they suffered financially and academically as a result. The OIA's intervention led to the university refunding two-thirds of the MA course fee to the students.

The ombudsman said it received more than 2,000 appeals against intramural decisions in 2012, up from the 1,600 received the previous year. Students are only able to take complaints to the OIA once they have exhausted internal complaints and procedures.

"The increase in fees means that students are clearly demanding more from their universities. The important thing is ensuring that students have enough information about their courses and that the experience matches their expectations," said Eric Thomas, the vice chancellor of Bristol University and president of the Universities UK group.

Of the total appeals received, the OIA dismissed nearly three-fifths as "not justified", while 17% of cases were outside the OIA's remit. But 18% of all the appeals were decided in favour of the complainant in one form or another: 6% were settled, 8% were judged to be partly justified, and 4% were justified.

"It must be remembered that these total about 300 complaints, from a student population of over two million students," Thomas said.

"While there has been a net increase in the number of complaints, we must not lose sight of the fact that the vast majority of students are satisfied and satisfaction rates across universities remain high."

The majority of complaints regarded "academic status", which included degree class and grades.

Business students were the most likely to make appeals, ahead of law and medical students.

Undergraduates were the source of two-thirds of complaints overall.

One complaint was ruled to be justified when the OIA found a university did not investigate "significant allegations about possible malpractice on the part of academics with appropriate objectivity and openness. The university's documents indicated that a strong impression was given to the student that they might be treated less favourably due to these allegations."

In another example, the OIA upheld a complaint by a PhD student that the university's examiners did not understand his subject.