Otago University was ranked the country's overall most research-intensive university - just ahead of Auckland - in the previous PBRF quality evaluation round, in 2006.
In the latest round, Auckland and Otago universities are both behind Victoria University, of Wellington, which was ranked fourth last time. Victoria scored 5.51, Auckland 5.12 and Otago 4.96.
The Tertiary Education Commission (TEC) co-ordinates the quality evaluation rounds, which help determine Government research funding for universities and other tertiary institutions.
A total of $262.5 million is being allocated this year. The Government plans to increase the PBRF to $300 million in coming years.
In ''indicative funding'' signalled in the latest PBRF report, published yesterday, Auckland University received $80.3 million, 30.6% of the overall allocation.
Otago University gained the second-highest funding, $53.38 million (20.43%). This was well ahead of Massey University ($34.5 million), Victoria ($26.9 million) and Canterbury
($24.58 million).
Otago University deputy vice-chancellor, research and enterprise, Prof Richard Blaikie, said the evaluation established Otago's 20.3% of overall annual PBRF funding.
As the overall funding pool continued to rise, Otago's $53.3 million share could be expected to reach about $60 million within the next few years.
The overall results reflected ''remarkable gains in research productivity'' by both Otago University and other New Zealand universities since 2006.
There were some ''disappointing'' aspects to the latest evaluation outcome.
Further efforts would be made to identify areas where Otago University could further improve its research performance, Prof Blaikie said in an interview.
But Otago researchers had made ''outstanding'' efforts, resulting in a further big increase in performance since 2006.
Instead of making its evaluation from a single overall average quality score measure, as in 2006, TEC had this time used four different average quality measures, and Otago had improved its performance in all four, he said.
Otago University is the country's only university ranked in the top four places across all measures, including topping the country in a measure of research quality weighted by its postgraduate student roll - ahead of Lincoln and Victoria universities.
Otago also came second in another quality measure weighted by degree-level enrolments.
The intensity of research-related competition between the country's leading universities can be seen from the fact that although Otago University had 18% more publicly-funded staff evidence portfolios than in 2006, it actually gained a lower relative ranking.
Prof Blaikie praised a particularly strong research performance by the staff at the university's Christchurch campus.
Otago University was ranked number one in four of the 10 highest-ranked PBRF academic disciplines in the country: pure and applied mathematics, philosophy, law and pharmacy.
Otago Polytechnic performed strongly in the latest Performance Based Research Fund evaluation round, nearly doubling its annual PBRF income from about $660,000 from 2006 to $1.14 million per year over the next six years.
The polytechnic has also been ranked third in the country in the institutes of technology and polytechnics sector.
Polytechnic research and enterprise director Alistair Regan said the results were a ''positive endorsement'' of the efforts the polytechnic had made to ensure it could address ''real concerns facing the community''. In the latest round, 62 polytechnic staff had achieved a PBRF rating, up from 45 in 2006.
PBRF-rated staff in the School of Design had doubled, to 16, and the school was ranked fourth in the entire tertiary sector, including universities.
And the Dunedin School of Art had been ranked fifth in the tertiary sector for the quality of research outputs, he said.
