"The biggest problem is that our students quite simply can't get into Sweden," said Malmö University administrator Kjell Gunnarsson to Sveriges Radio (SR).
Gunnarsson estimates that between 40 and 50 non-European students who have already paid fees to secure their places at Malmö University may miss the start of the fall term because they haven't received visas.
The problem stems from a new EU-directive which requires non-Europeans to be photographed and submit fingerprints in order to receive a special residence permit.
Currently, not all Swedish embassies are equipped with the proper machinery to collect and process the information, forcing many would-be students to undertake long and expensive trips.
"They may have to travel from Trinidad to Washington, DC two times in order to submit and pick up their visa," Gunnarsson told SR.
"Students who are in Fiji are directed to Australia. It's not a dignified way to treat students."
He added that other European countries, such as Italy, chose to implement the rules in a way that allowed students to leave biometric information upon arrival in the country.
Migration minister Tobias Billström told SR he had not previously been aware of the issue, but promised to investigate it further.
He added that the problem affected not only students, but anyone seeking a residence permit who is also required to submit biometric information.
"When you implement a chance it's impossible to avoid a transition period," he said.