Footage showing a Northland dairy farmer violently and repeatedly hitting cows with various weapons including a steel pipe have been given to the Ministry for Primary Industries.
MPI has already investigated the claims but the inquiry was dropped because of a lack of evidence.
Farm animal advocacy group Farmwatch has been gathering evidence since May and passed fresh evidence to the ministry last Thursday, asking it to do another investigation.
Gary Orr, acting director, compliance services confirmed the ministry has received the complaint and said an investigation was under way.
"MPI began an immediate investigation as soon as it received the footage last Thursday," Orr said.
"As this is an active investigation, we cannot comment further at this stage."
The footage showed the animals being hit on the head and legs with farm tools and weapons.
"Watching the footage is heartbreaking, and you can see the animals scared and terrified to go into the milking shed. They visibly cower when the farmer is near," Farmwatch spokesman John Darroch told the Herald.
Darroch said the case was not the worst, but it was "at the worst of the spectrum" that he has seen as a volunteer investigator.
"The video is shocking and deeply upsetting to watch," he said.
"Unfortunately animal abuse in New Zealand farms is far more common than people believe."
He said numerous complaints have been made to MPI about the abuse, and MPI had the responsibility to do a thorough investigation.
"The public needs to have confidence from both MPI and the dairy industry that animal abuse isn't happening," Darroch said.
DairyNZ's strategy leader Dr Jenny Jago said the wellbeing of animals must be "at the heart" of every dairy farm.
"It is not okay to treat any animal poorly - ever - and the vast majority of farmers care deeply about their animals," Jago said.
"This footage is disturbing ... this type of appalling behaviour is absolutely not representative of the thousands of farmers that work with cows every day and are passionate about animal welfare."
Jago said cruel and illegal practices are not condoned or accepted by the dairy sector as part of dairy farming.
"If a farmer treats their cows badly, they shouldn't be working in the dairy sector. It's as simple as that."
Animal advocacy group Safe was first alerted about the farmer when a photo was shared of a cow spray-painted with the words, "I am an a***hole".
The image was shared on the NZ Farming Facebook page and many complaints of physical abuse of cows were received about the farmer who had written the message.
"Farmed animals are clearly not safe when MPI doesn't carry out an effective investigation even when brave whistleblowers risk themselves by making complaints," said head of campaigns Marianne Macdonald.
"The system supposed to protect animal welfare is broken."
Macdonald said MPI's failings were "beyond belief".
A previous inquiry - where the video footage showed the sharemilker moving cows on dairy farms by hitting them on the rump with an alkathene pipe - was dropped by MPI due to a lack of evidence.
A Newsroom journalist who visited the farm was told by the man that he hit the cows to train them, and that the best approach was to be "kind and firm".
Two former staff from the farm told the reporter they had witnessed the man abusing cows, and one former farmhand said it was the worst milking shed he had been in during his 20-year career.