Students from Glasgow University found they were unable to register for courses through the controversial MyCampus system.
Some took to social networking sites such as Twitter to complain, with one stating: "Another splendid display of incompetency from Glasgow Uni. Bravo."
"Don't even see the point in attempting to enrol for 4th year. MyCampus is a joke," stated another.
Another said: "The only thing you can rely on with MyCampus is its consistent ability to fail to provide its most basic services. Like enrolling to classes."
Officials said it was unclear how many students are affected, or what the underlying problem is.
The university went on to apologise and advised students to wait for an official email from the university before trying to re-register.
An urgent investigation is being carried out to find out why students cannot register.
A university spokeswoman said: "A number of students have experienced problems today when trying to register online for the next academic session.
"The university is sorry for any inconvenience caused and is urgently investigating the reason for the problem.
"We will advise all students as soon as this is resolved."
Last year, thousands of students called a university helpline to complain about glitches that left them unable to register for courses following the introduction of the MyCampus system.
Common complaints included students being enrolled for the wrong degree or told compulsory classes were full. Others complained about web links not working.
Students were advised by some university tutors to ignore the system and simply turn up at the correct classes, while other tutors have had to write out timetables by hand.
Following the debacle, computer specialists from the university warned the disruption was likely to be repeated this year because of flaws in the system.
An email summarising the view of computer science specialists described the controversial system as "unintuitive, riddled with errors and extremely difficult to use".
It added: "This is not a teething problem and therefore likely to recur every year."
The MyCampus system is designed to support students throughout their studies and has already adopted by Cambridge, Queen's University Belfast and Derby University.
The university argues it is vital as it allows students to enrol and select course options online, as well as paying fees. The information can then be used to analyse key statistics such as applications, exam performance and retention rates.
MyCampus was installed to replace the existing in-house system, WebSurf.
The UCU lecturers' union believes WebSurf is effective and has described the new system as "cumbersome, frustrating and unreliable".
Course advisers say the introduction of MyCampus has increased their workload because they have been inundated with queries from worried students.
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