A report analysing how AgResearch formed a plan to shift 80 jobs from its Invermay facility in Dunedin to Lincoln is highly critical of the Crown Research Institute.
Dunedin City Council commissioned the report from BERL, an economic research consultancy.
It says the report shows serious shortcomings in the justification for the move and what the economic benefits might be.
AgResearch had suggested moving Invermay's research activities to Lincoln and Palmerston North would save money, but the report says the methodology used to support that claim was tenuous and convoluted.
It also criticises AgResearch's lack of investigation of alternative options, but stops short of saying the Crown Research Institute had a pre-determined position in mind.
However, Science and Innovation Minister Steven Joyce is questioning the objectivity of the report and BERL's independence.
He says the agency tends to uncritically support the view of those who commission reports.
Mr Joyce says it would be better if the Dunedin City Council engaged directly with the AgResearch board, whose job it is to assess the economic case for the shift.