In 2011, 483 Malaysian students were enrolled at Otago, the university's second largest cohort of overseas students.
This week, Malaysian low-cost carrier AirAsia X confirmed it will end direct flights between Christchurch and Kuala Lumpur at the end of May.
Otago University pro-vice-chancellor (international) Prof Sarah Todd said ease and cost were factored into decisions made by students but there was no evidence to suggest the university's Malaysian community would shrink.
"Accessibility and affordability are both important factors in international students' decision-making. However, we have long had large cohorts of Malaysian students at Otago, and no increase in their number has been noted in the time that AirAsia has been flying into Christchurch, so it is not possible to say what, if any, impact the cutting of the Christchurch route will have on international student numbers," she said.
AirAsia X is working with other airlines to help travellers booked after May.
The last flights take off on May 30, from Kuala Lumpur and May 31, from Christchurch.