The Tertiary Education Commission this week released a report by KPMG, which revealed a number of issues in the way institutions carry out the performance-based research fund (PBRF) process.
PBRF rankings are calculated by awarding academic staff gradings and points for the quantity and quality of their research.
Universities use their ranking as a marketing tool to attract students and staff.
The University of Otago topped the most recent round in 2006 with 4.22 (out of 10), a smidgen ahead of longtime rivals Auckland University on 4.19 and Canterbury University on 4.10. The next round is scheduled to take place this year.
Union national president Dr Sandra Grey said the report confirmed their view that universities were "gaming" the PBRF process.
"Universities have changed people's employment agreements, restructured departments and people's jobs and in some cases made academics redundant simply so that they can appear higher on a rankings ladder than other universities, " Dr Grey said.
Among the concerns raised by the report were that institutions were not including staff in the PBRF process due to incorrectly calculating their full-time equivalent status and that institutions were excluding large proportions of staff on the basis they were under "strict supervision".
The audit showed the proportion of staff excluded on the basis they were under "strict supervision" was much higher at Otago University (32.4%) than other institutions. Auckland University had the next highest proportion, with 19.3% under "strict supervision".
Dr Grey said putting staff under "strict supervision" could be used as a way to "hide" staff the university considered would compare poorly in terms of research output.
TEC general manager of strategy, planning and information David Nicholson said it was taking the issues raised in the audit seriously and was concerned the way institutions managed their staff could affect their ranking on league tables.
"We are now consulting with the sector to determine if there is a more meaningful way to report the [league tables]," he said.
Dr Grey applauded the commission for releasing the results of the audit and looking into ways to end the "gaming" of the system, but said the process came too late for staff who had already lost their jobs because institutions wanted to manipulate their quality ranking.
The Otago University was unable to comment because key leaders were on leave.
