The MPI investigation followed a complaint about the state of starving calves on the farm.
The judge said that under the Animal Welfare Act the onus was on Harcourt to prove he did "all" that he was ordered to do by the MPI -- noting that much of his defence had been to deflect blame on to the ministry and others.
However, Harcourt had failed to follow a notice issued to him to take "all reasonable steps" to follow the steps ordered by the MPI.
These included to de-stock, seek veterinarian advice and treat animals, and to follow advice to feed his cows 16kg of dry matter per cow per day.
"The defendant was obliged to prove he had taken all reasonable steps," the judge said.
The judge also commented on the "collateral issue" of Harcourt's milk supply contract being cancelled by Westland Milk Products, in mid-October 2012.
"It is evident that Mr Harcourt believes that the suspension of his contract with Westland Milk Products was solely down to the MPI," Judge Saunders said.
However, the judge did not accept that. He would release a full written finding in due course.
Judge Saunders adjourned the hearing until October 12 to ascertain MPI investigation and court costs, and to weigh up what fine Harcourt would have to pay.