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AgResearch says ''very little'' of its work with the University of Otago is based at Invermay.
This comes after Science and Innovation Minister Steven Joyce said this week opportunities had been lost to strengthen research links between the two institutions.
There had been plans for more co-operation between the two when the new Christie Building was constructed at Invermay in 2008, Mr Joyce said.
Collaboration between Otago University and Invermay, particularly around genetics, has been a major part of arguments against AgResearch's plans to cut about 80 jobs from the facility.
A spokesman for AgResearch agreed plans for more collaboration out of the Christie Building did not work out as envisaged.
''It is no secret that the collaboration envisaged in the initial proposals and development of the Christie Building has not materialised as well as either party would have preferred.''
The spokesman also said its collaboration with Otago University was spread across all its campuses.
''Very little of our current work with Otago is based at or led from Invermay. It contributes to our national science programmes.
''AgResearch has a positive, collaborative relationship with the University of Otago across all of our campuses, and as we do with tertiary education and research institutions around the country.''
Otago University did not respond to questions on its level of collaboration with Invermay.
However, when asked about the Christie Building last week, deputy vice-chancellor, research and enterprise Prof Richard Blaikie said: ''It's quite simplistic to say [the Christie Building] was a collaboration. It was an AgResearch decision to invest in the building.''
Both Prof Blaikie and AgResearch did not comment on the suggestion that issues over the amount AgResearch charged for university scientists to be based at the Christie Building was why it had not been successful.