The University of Otago ranked third, followed by the University of Canterbury, University of Waikato, Massey University, Lincoln University, Auckland University of Technology (AUT) and Unitec.
In releasing the rankings, the TEC noted that they did not represent the quality of a university, as other aspects such as teaching or course content were not measured.
Universities also vary in the quality across subject areas.
Yesterday, University of Auckland vice-chancellor Professor Stuart McCutcheon said its second-place ranking was "apparently counter-intuitive".
He said the PBRF had confirmed the university as the country's leading research institution.
It had secured the largest share of the fund, with $80.4 million or 30.6 per cent of the national total, reflecting its dominance in the three core components of the PBRF.
Mr McCutcheon said the change in rankings reflected a new method in calculation. For example, the postgraduate component divided the quality parameter by the number of postgraduate students enrolled - which had disadvantaged Auckland because it had grown its programme.
"We are interested in the productivity of the university by international standards, and so the average quality score is not a big issue as far as we are concerned."
AUT vice-chancellor Derek McCormack said because the rankings were based on average scores they were "spurious".
He said that despite maintaining its ranking of eighth, AUT had more than doubled its funding and research-active staff in the latest round.
Tertiary research
2012 Quality Evaluation ranking:
1. Victoria University
2. University of Auckland
3. University of Otago
4. University of Canterbury
5. University of Waikato
6. Massey University
7. Lincoln University
8. Auckland University of Technology
9. Unitec
Source: The Tertiary Education Commission.
