People for the Ethical Treatment of Animals (Peta) also seemed to dispute suggestions it was too slow to be upfront about what it was documenting.
"We conduct thorough investigations to uncover the true nature of an industry, not isolated incidents," Peta Asia senior vice-president Jason Baker said.
"Unfortunately, everything we documented reflects standard practices.
"We consistently raise concerns directly on-site."
Peta said it went to 11 shearing sheds and farms — including one high-profile example in Central Otago — and this showed shearers "kicked, beat, and stomped on sheep and threw them down chutes", among other disturbing scenes.
It labelled the New Zealand Merino Company’s ZQ ethical wool certification programme a sham and passed on footage and information to the Ministry for Primary Industries, which is investigating.
MPI noted some allegations went back to 2023.
Lawyer and shearer Jills Angus Burney told The New Zealand Herald the people who shot the footage shared by Peta should have reported what they saw immediately.
It also seemed to be "cherry-picking" its findings, she said.
Mr Baker said acts such as punching, kicking and hitting sheep were disturbingly common.
"Our complaint [to MPI] comprised 71 pages and included many hours of footage," he said.
"The full details are now with the government for investigation."
Peta described shearing as "a painful, frightening ordeal for sensitive and cautious sheep" and it said most sheep were left bruised and bleeding.
"Regardless of what action the government may or may not take, the evidence is clear — the only way to ensure you are not contributing to sheep abuse is to not buy wool," Mr Baker said.
The organisation opposes "speciesism, a human-supremacist world view".
Federated Farmers meat and wool chairman Toby Williams said Peta had an extreme anti-farming agenda.
"In reality, what you’re seeing in that video is a montage showing some isolated examples of poor practice that most Kiwi farmers simply wouldn’t put up with in their shearing shed."
New Zealand farmers had high animal welfare standards and shearing was for animal health and wellbeing, he said.
"We want to prevent issues like fly strike and heat stress over the summer months."
The New Zealand Merino Company said the ZQ programme was introduced to improve animal welfare.
Its principles included fostering freedom from pain, distress, injury or disease.
The company said it did not tolerate breaches of animal welfare guidelines and any accredited farms in breach risked action "up to and including expulsion from the programme".
Former American television show host Matt Lauer’s property near Lake Hāwea was linked by Peta to alleged abuse by contracted shearers.
The Cochrane family runs Hunter Valley Farming there and the company released a statement this week.
It took animal welfare seriously and the company and its independent contractors must adhere to standards and procedures under New Zealand law, a spokesman said.
"We are currently investigating the allegations we have received from Peta with the independent contractors undertaking the shearing activity."
Advice was being sought from MPI.
"We have also made Mr Lauer aware of this situation and continue to keep him updated," the company spokesman said.
