However, he noted the university remained "in a period which is amongst the most difficult time in at least two decades in which to forecast with confidence".
"Global uncertainty remains a significant factor, and the extent to which the aftermath of the Canterbury earthquake will continue to impact on enrolments is difficult to call with great confidence," he said.
The predicted 18,918 EFTS was still below the 18,951 enrolled at the university last year, and 3.8 per cent below the university's peak of 19,661 students in 2010.
Changes to student loans and allowances access and the introduction of limitation of enrolments had impacted domestic enrolments in recent years, Mr Thomson said.
Financial services director Grant McKenzie said setting next year's budget had been a "challenging process".
"Trying to achieve a balance between maintaining an adequate operating surplus and ensuring that the academic departments have adequate resources deliver their outputs was difficult."
"The outcome is a surplus that meets the minimum guidelines set by the Tertiary Education Commission but is less than council's approved fiscal strategy."
Despite the challenges the university's financial position continued to be "strong with no external debt".
For next year the university was expecting an operating surplus of $20.597 million which was down on the forecast surplus of $21.375 million this year.
Speaking at yesterday's meeting, Mr McKenzie said factors, including the timing of insurance proceeds from Christchurch's earthquake, could make this year's surplus climb higher than the forecast figure.
Mr McKenzie is taking up the role as Dunedin City Council group financial manager in January.
Asked by council member Michael Sidey if there was anything the council needed to be careful of in future years, Mr McKenzie noted significant spending on planned new buildings planned would decrease the amount of cash on hand - which had provided a significant amount of investment income for the university in recent times.
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