Mr Johnstone was charged after MPI staff visited his properties in 2014 to inspect skinny calves after a complaint.
The Ministry said its staff found several animal welfare issues on Mr Johnstone's properties and did what they could to mitigate the animals' suffering.
"The issues include a mob of skinny weaner calves in a paddock without grass or water, an emaciated young cow having difficulty standing, which had to be put down, and finding two calves that had died from starvation."
Mr Johnstone told NZME News Service he was advised not to fight the charges.
Mr Johnstone said two droughts in the region and a shortage of hay had made life difficult for farmers.
He said "everybody" had one or two sick animals.
"We all have an odd beast get crook and something happens," he said.
"We've got no hospital for sick cattle. But they've got a hospital for sick people."
He had mixed feelings about MPI inspectors, but he said he accepted MPI had a job to do.
He said he would not appeal and would pay the fine as ordered. He was now busy selling his animals. He expected his son to take over the farm.
"I want to retire. I want to go on a cruise, on a boat. I've worked hard all my life."
Mr Johnstone will be 102 years old before he is eligible to own, control or have any authority over production animals.
MPI said the court heard Johnstone had a history of similar offending and was disqualified from owning or managing stock for two years in 1997.
