The owner of a Waikato-based pet food company accused of abusing bobby calves will face trial by jury.

Alan Martyn Cleaver, 57, has pleaded not guilty to four charges at the Huntly District Court laid against him by the Ministry for Primary Industries.

Cleaver, who was excused from attending court on Wednesday, has previously said he felt his now-defunct company Down Cow Ltd was used as the scapegoat after footage of animal abuse by one of his employees went public.

The recordings were made by Farmwatch and welfare organisation Save Animals From Exploitation.

Cleaver pleaded not guilty to two charges against him, and two charges as owner of Down Cow.

One charge, under the Animal Welfare Act, alleges he failed to meet calves' physical, health and behavioural needs by using and allowing blunt force trauma on calves.

That charge carries a maximum penalty of 12 months prison and and a $50,000 fine.

A second charge of not supporting animal welfare procedures carries a maximum $250,000 fine.

Cleaver was remanded on bail and reappear for a pretrial hearing on February 8th.

Down Cow shut down on May 18, which Cleaver claims was due to unattainable requirements set by MPI.

He said his company was unfairly targeted and penalised for procedures which he claims were common and sometimes necessary among the country's farmers and slaughterhouses.

But MPI has defended itself, saying it didn't force the company to close, but gave it notices of compliance.