Exam materials were held in a secure area of the Clocktower building.
The vast majority of stolen exams had been sat by the students on Saturday, and their scripts were unmarked.
Deputy vice-chancellor academic, Prof Vernon Squire, said university staff were contacting each of the 98 students who had their exam scripts stolen.
Prof Squire said his immediate concern was for the students who have been affected.
"We understand how upsetting and disappointing this is for the students.
"The considerable effort they have put into their study and exams has essentially been ruined by this reprehensible criminal act," Prof Squire said.
"We will do all that we can to support the students."
A range of different subjects was involved and the students were at different stages of their courses.
"It is our hope that the scripts will be returned, but at this point we need to put plans in place as this may not occur.
"Therefore, we are making arrangements with the students to prepare for a likelihood that their scripts will not be returned," Prof Squire said.
"We remain hopeful that this crime can be resolved."
Planning and effort had "gone into this act" and there may well be people in the North Dunedin area who had information that "could help the police in their investigation", he said.
"I strongly urge anyone with information to contact the police as soon as possible," he said.
Dunedin police can be reached on 03 471 4800. Alternatively, information can also be provided anonymously via the organisation Crimestoppers on 0800 555 111.