Farm animal advocacy group Farmwatch has been gathering evidence since May and passed fresh evidence to MPI last week.
The footage shows the animals being hit on the head and legs with farm tools and weapons including steel pipe.
Whaitiri today unveiled a new framework for animal welfare, setting out what she said would be a clearer, more transparent and inclusive system. Capacity-building was a key part of the framework.
"I have a limited number of animal welfare officers at MPI and one of my issues is to make sure we are beefing that up so that investigations can happen a lot more quickly.
"I also want to build relationships with people working in the regions, particularly around animal shelters, to see how we can actually work in tandem to improve these outcomes.
"I think this reset will be very clear to animal advocate groups and industry people that this Government is serious around improving animal welfare outcomes."
She is expecting a briefing next week on how MPI investigates animal cruelty cases.
"I think we've got room to improve. Ultimately, as I've said in this framework, resourcing is going to be a critical issue because you can only do what you can if you've got only limited people on the ground.
"We got to think how we do things smarter in partnership with others, to make sure that kind of practice is absolutely removed by not only our farmers but all those who have animals."
Animal Advocacy group Safe's head of campaigns Marianne Macdonald said farm animals were not safe when MPI didn't carry out effective investigations.
She said MPI's failings were "beyond belief".
MPI has been approached for comment.
The Dairy Companies Association of New Zealand said today it supported MPI taking strong compliance action in the latest case.
"Animal welfare is of utmost importance to New Zealand dairy companies," said Kimberly Crewther, the association's executive director.
"There is no excuse for mistreatment of animals and no place for those who mistreat animals in our industry."
