The University of Waikato has revealed a $16.8 million deficit for 2022.
The result means six of the eight universities made financial losses last year.
The university provided RNZ with the details, before its annual report is published next month.
It said enrolments dropped 4 percent last year after a surge in enrolments in 2021.
It had 10,119 full-time equivalent students - including 1637 foreign students, 700 of which were offshore.
The university succeeded in attracting about the normal number of school-leavers last year but it found that many of the students who enrolled in 2021 had enrolled in one-year masters degrees and did not re-enrol for 2022, the report said.
The report said the university would have to repay $748,500 to the Tertiary Education Commission because its enrolments were 98.1 percent of its funding allocation, just shy of the benchmark of 99 percent for avoiding repayment.
The university's vice-chancellor Neil Quigley told RNZ contributing $11.2m to the deficit were one-off factors including a change in accounting treatment of computer software ($4.6m), a loss from investments made by the university's foundation ($1.3m), increased depreciation ($2m), and restructuring costs ($3.3m).
"The regular operational loss for the year is $5.6m which is somewhat in the range that we had expected," he said.
"A key challenge is that we don't have changes in our funding, particularly our government funding to compensate for those sorts of things," he said.
He said the university wanted to break even this year but was likely to make a small deficit.