The University of Canterbury recorded a 5% drop in its enrolment figures from new students, alongside a 10% drop in applications from international students for the 2012 academic year.
The university is forecasting domestic full-time equivalent student numbers for the full year, including second-semester enrolments, to drop by 1.7% compared to last year, and to be 13% lower than before the earthquakes started, in September 2010.
Meanwhile, the number of first-year students from the Canterbury region enrolling at Otago University had increased by 16.4% from 524 in 2011 to 610 in 2012.
This is significantly higher than the overall increase in domestic first-year enrolments of 5.4%.
The number of students transferring to the university from the Canterbury region had risen by 17.9% from 112 in 2011 to 132 this year.
Otago University director of planning and funding David Thomson said the figures suggested the earthquake had resulted in a "modest increase" in the number of students coming to the university from Canterbury.
Following last year's earthquake Otago University put in place a policy which allowed residential colleges to take into account the quake's impact when considering applications from students, including impacts on academic performance.
The colleges also provided support for students who moved down from Canterbury because of the quakes, Mr Thomson said.
First-year health sciences student Tony Kim, a resident at Arana College who came to Otago University from Christ's College, said he had a couple of friends who came to study in Dunedin to be away from the aftershocks.
He said it was a good to be away from the threat of more quakes, but because he was studying health sciences, he was always going to move away from Christchurch.
Fellow Arana College resident and first-year anthropology student Lara Richards, who came to Otago University from Christchurch Girls' High School, said she had always planned to study in Dunedin but the earthquakes reinforced her decision.
The decline in students and staff members meant the quality of education at the University of Canterbury had dropped, she said.
"It just seemed like I would be limiting my chances if I decided to go [to Canterbury]," she said.
Both students said they had received a warm welcome in Dunedin.
Otago Polytechnic communications co-ordinator Emma Wood said there had been an increase in the number of students coming to the institution from Canterbury, with the province making up 10.6% of all high-school leavers to enrol in the polytechnic this year, compared to 7.5% last year.
As of mid-December last year, 4.3% of the total applications from prospective students at Otago Polytechnic were from Christchurch residents.
The figure was up from the 3.31% of Christchurch students who applied to study at Otago Polytechnic in the 2011 academic year.