AgResearch is making only small changes to its controversial Future Footprint programme, after months of consultation with farmers and community leaders.
The Crown Research Institute's $100 million programme will shift about 150 scientists and 100 administration jobs, mainly from the Hamilton and Invermay campuses to two new science hubs in Lincoln and Palmerston North.
The plan was first announced a year ago and on Thursday AgResearch confirmed it, saying it was now moving into the "design phase".
Otago and Southland leaders, as well as farmers, have waged a campaign to stop 75 staff, especially the animal genomics team at Invermay, near Dunedin, being moving north to Canterbury.
AgResearch said it has made changes which will keep five more staff at Invermay. These include keeping three deer researchers in the south and it will retain the Invermay and Ballantrae hill farms.
The University of Otago would also be co-locating between five and 10 of its genomics staff and sequencing equipment at the Invermay campus.
Pete Hodgson, a former science minister, said on Thursday that AgResearch is making a bad decision.
"I find it astonishingly foolish that they would have confirmed their earlier decision. They are walking away from the most powerful genetics capability in New Zealand and, in fact, in Australasia. They are walking towards a genetics capability in Lincoln which is extremely skinny."
Mr Hodgson said AgResearch is repeating the mistakes of past failed relocations.