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Dr Clark said revelations AgResearch had failed to meet worst-case scenario deadlines for selling farms showed its restructuring plan was a ''shambles''.
He said Mr Joyce's written answers to parliamentary questions showed AgResearch had failed to meet its deadlines for selling four of its research farms in order to fund its restructuring plan.
''In AgResearch's `worst case' scenario, the sale of Flock House was to be completed by June last year, and Kaitoke was due to be completed this month. They have not been,'' Dr Clark said.
An AgResearch spokesman said Dr Clark's claims were based on out-of-date information and that it now planned to sell ''a number of our farms by 2016''.
An agreement in principle for the sale of its Flock House farm, near Bulls, had been made with the Ngati Apa tribe.
Mr Joyce said Dr Clark's criticisms of every aspect of AgResearch's operations were now wholly political.
''I would no sooner judge progress by Dr Clark's view than fly to the moon,'' he said.
Asked if he was concerned about the recent revelation four ''star'' scientists intended not to shift from Invermay to Lincoln, he said: ''Staffing matters are appropriately managed by AgResearch.''
''The [AgResearch] board is failing to manage project risk.
''AgResearch's board and Minister Joyce have already agreed that staff retention is the No 1 risk to be managed. And they are failing there, too.''Add to this the fact that 92% of sheep breeders are against the plan, and you have an emerging debacle.''
Dr Clark stood by his comments after being told AgResearch had changed its timeline for the sale of its farms, saying it ''begs the question how many times they are going to shift the goal posts''.
An AgResearch spokesman said progress on farm sales was on track.
''The estimations from 2012 have been replaced by those in our statement of corporate intent and project plan,'' he said.
The sales had no effect on its plan to move about 75 Invermay staff north to Lincoln over the next three to four years.
There was ''no basis ... whatsoever'' to Dr Clark's claim AgResearch's restructuring plan was an ''emerging debacle''.
In a report given to the Otago Daily Times under the Official Information Act last year, a Ministry of Business, Innovation and Employment official said it believed AgResearch's timing of asset sales to be optimistic.