In a separate case, MPI also charged a farmer over allegations of transporting a cow while it was suspended from a hip clamp.
The farmer is scheduled to appear before the Morrinsville District Court in February.
Meanwhile, Down Cow - a Waikato pet food processing plant - and its company director Alan Cleaver are defending their charges. Their case remains before the court.
The charges follow a prosecution earlier this year in which Noel Erickson, an employee of Down Cow, was jailed for two years for the abuse of bobby calves.
Slaughterman Erickson admitted his role in the abuse which involved him kicking and hitting calves and dragging one under a gate.
Erickson was initially sentenced to 10 months' home detention but the sentence was overturned for a jail sentence in November after MPI won an appeal.
He will now serve two years in prison.
Judge Patricia Courtney said the original decision took into account Erickson's lack of training and supervision, but that his culpability was not "markedly" less because of this.
"It was simply a cruel disregard for the animals' welfare," said Judge Courtney.
"It is undeniable that Mr Erickson's offending was callous and brutal, and caused suffering to very young and vulnerable animals."
The abuse was brought to light after Farmwatch secretly filmed Erickson in a hidden camera sting.
MPI launched a probe last September following release of the footage.
Save Animals From Exploitation [Safe] spokesperson Mandy Carter said although it was pleasing to see two other people charged she was disappointed that the prosecution was being dragged out for so long.
She now hoped that MPI would take the issue of bobby calf mistreatment seriously.
"Just because they prosecuted a few people ... it doesn't mean that these things won't happen again in the future so they really need to take a proper concerted effort to make sure this doesn't happen again."
Since giving the footage to MPI, a source confirmed 17 investigations have been launched.
Along with Erickson and Cleaver, three others received formal warnings relating to leaving calves in crates all day, while another slaughterhouse employee was warned.
Four bobby calf loaders were officially warned while five others received no further action.
A haulage company has taken part in an education day from an MPI inspector at its own request.
