"We don't want to be seen as kicking a man when he is down," Mr Fletcher said.
Officials first visited Harcourt's 680ha farm at Crooked River on September 13, 2012, after a complaint about skinny and under-condition calves on the property.
It was later forced to intervene and 77 cows had to be slaughtered.
During the first visit an MPI inspector found about 740 head of stock, including about 540 in-milk dairy cows, plus empty or un-calved cows, young stock and calves. A significant number were under weight or emaciated.
A veterinarian subsequently found 72 calves "stunted in growth". The calves were visibly "shaking" with a heavy "parasitic burden" of worms.
At the time, about 10 days worth of feed was estimated to be left on the farm to feed all the stock.
"The property was overstocked," Mr Fletcher said.
Harcourt was given room to fix the situation, including a feed plan and de-stocking.
"As this matter progressed Mr Harcourt received direction to increase the feed to his cows, and he did not follow that direction."
A "significant resource" was required to rectify the situation, in the end, Mr Fletcher said.
On September 20, MPI district compliance officer Peter Hyde returned to the property with farm consultant Richard Reynolds.
Harcourt was ordered then to feed 16kg of dry matter per cow per day; the ministry later found that Harcourt had purchased 28 tonnes of palm kernel and by September 30 "the situation was getting back under control".
However, by October 11 he was not feeding out the supplement and there was evidence of only a small amount of the palm kernel having been used, Mr Fletcher said.
On October 24-25, 2012, an MPI operation identified 77 emaciated cows, which were sent for emergency slaughter at the Kokiri meatworks.
Mr Fletcher said the ministry learned then that the freezing works had already noted a "significantly higher than normal rate" of emaciated animals arriving from Harcourt's farm.
He said the MPI would provide evidence of "a deteriorating relationship" with Harcourt.
Later in the hearing, Mr Hyde outlined discussions with Westland Milk Products after it advised the ministry it was going to cut milk collection from Harcourt.
"The general tenor was around welfare issues, and also effluent issues."
"Threats" by Harcourt to Westland Milk staff were also discussed, Mr Hyde said.
The ministry outlined its concerns to Westland Milk about the impact on animal welfare from suddenly stopping milking cows, such as mastitis, and the environmental issue of dumping milk.
It subsequently heard that the dairy company had been saying the MPI had ordered it to cut off Harcourt, "that WMP had told people in the community that MPI had directed it to stop collecting milk from Donald Harcourt".
Mr Hyde said he subsequently spoke with the company to refute that, then wrote to the company to say "we did not direct WMP to stop collecting".
The case is continuing.
