Judge Phillip Cooper said that on December 6, 2015, Whatmough arranged through a livestock agent for 42 cows to be trucked from his farm to an abattoir in Hamilton.
He left a farmhand in charge of loading the animals but gave no clear instructions about which animals, if any, were unfit to be loaded, the judge said.
Two cows died during the six-hour journey, two others were put down on arrival and two more were declared unfit for transport.
The ministry said those responsible for the welfare of dairy cattle must be competent at recognising ill-health or injury and take remedial action as required.
Ministry documents stated that Whatmough claimed to have inspected 39 of the 42 animals and knew three cows were unsuitable for transport.
He said he did not know what was wrong with them except that they were not very healthy.
Whatmough did not obtain a veterinarian's certificate before the cows were transported.
He expressed remorse and insight into his offending and said he had put in place measures to ensure there was no repeat. He had no previous convictions.
Judge Cooper fined him $1500 on each charge and also ordered him to pay $150 court costs. Ill-treating animals carries a penalty of 12 months in jail or a $50,000 fine or both.
The charge of permitting unfit animals to be transported carries a similar penalty.
