The samples from the study, conducted by the institute in the capital Stockholm, were stored in a freezer system powered by liquid nitrogen.
But the system, which operates at -190 degrees Celsius, malfunctioned on December 22-23. The samples became unusable after a technical problem with the system that transfers liquid nitrogen to 16 refrigerated tanks, the university said on Monday.
The tanks can operate for another four days in case of failure, it said, adding that the samples were lost because the problem could not be resolved in time.
Matti Sallberg, dean of the institute's southern campus, said: "This happened at probably the worst conceivable time in Sweden, just one day before Christmas Eve."
The dean said that leukemia samples collected from patients for nearly 30 years were lost in the cooler failure. "They were also planned to be used for future studies," he said, pointing out that the samples play an important role in large-scale research.
Sallberg said that millions of Swedish kronor worth of samples had been lost, but did not give an exact figure for the losses.
Karolinska Institutet is home to the Nobel Assembly, which awards the Nobel Prize in Physiology and Medicine (AFP)
Swedish media reported that the value of the unusable samples was 500 million crowns.
Stating that they do not think that the problem is caused by any sabotage, Sallberg said that an investigation has been launched into the malfunction and the police are continuing their investigations.