Farmwatch investigator John Darroch said he saw deliberately cruel treatment of calves at about 15 of the 50 farms he secretly filmed across the Waikato.
"We saw calves being torn from their mothers and left in the hot sun for hour after hour, thrown into trucks and then beaten to death," he said.
- See the video here - Warning: contains graphic content
The footage, filmed undercover, was screened on TV One's Sunday programme last night.
Secret video recordings also showed bobby calves being kicked and thrown about at a slaughterhouse.
Between eight and 10 transport companies were filmed transporting calves -- and all treated them in a cruel manner, Mr Darroch said.
"I wasn't expecting to see this -- not in the slightest.
"We have been getting calls from people in rural communities -- including farmers -- for many years asking us to look into the treatment of bobby calves.
"But I had no idea that every time we posted a hidden camera we would get brutal treatment of calves. The scale and the frequency absolutely stunned me."
The footage, filmed in 2014 and this year across farms and a slaughterhouse in the Waikato, was screened on TV One's Sunday programme last night.
Mr Darroch said he wanted to expose what went on in farms, rather than to hurt farmers.
He suspected the mishandling of bobby calves had been going on forever, as they were considered a byproduct of the dairy industry.
"Calves being separated from their mothers at a day old is integral to the dairy industry -- we don't have dairy products without that. Even on the best farms with very high welfare standards, they're still pulling their babies away from the mother at a day old."
Consumers needed to think about whether they could accept this when they used dairy products.
DairyNZ chief executive Tim Mackle said cruel and illegal practices were not condoned by the industry.
"We are shocked and farmers are too," he said.
"We will be asking questions of everyone involved. Farmers don't see what goes on when calves leave their farm and we need to be holding the transport operators and processing plants to account to ensure bad practices get stamped out of our industry."
Federated Farmers spokesman Andrew Hoggard said the appalling behaviour was from a minority of farmers, transport companies and slaughterhouse workers and it was not something the industry would tolerate.
Hans Kriek, executive director of animal rights organisation SAFE said the video clearly showed the animals being abused.
He said more than 2 million bobby calves were killed each season, four days after being born, and were "literally left like rubbish, to be picked up at the side of the road".
"The moment we saw the footage we realised there was a serious problem happening especially at the slaughterhouse," he said.
Mr Kriek said a complaint was made and footage provided to the Ministry for Primary Industries on September 14, but there had been no response.
"It appears that MPI didn't even bother to visit," Mr Kriek said. "They were given hours and hours of hidden camera footage of the abuse."
Matt Stone, from MPI, told Sunday the ministry was investigating.
"We have initiated an investigation and I'm not going to comment further on our processes around that investigation," he said.
The owner of the slaughterhouse concerned claimed it had not been approached by MPI.
Fonterra group director co-operative affairs Miles Hurrell described the footage as "disgusting".
Mr Hurrell believed, however, that only a "small minority" of dairy farmers in New Zealand were guilty of animal cruelty.
"The vast majority of our farmers operate responsibly, and this is really sad to see this footage come to light," Mr Hurrell said.
Acting Prime Minister Bill English today said the revelations could embarrass the country's farming industry and warranted urgent attention.
"It must be investigated," Mr English told Paul Henry.
He said the Ministry for Primary Industries had the capacity to investigate and they "should get on with it".
He described the episodes of animal cruelty as "pretty awful" and not acceptable.
The farming community had a sophisticated understanding about what was required around animal welfare but these latest revelations threatened to cast a shadow over the whole industry.
It was also important the matter was thoroughly investigated given the key role the dairy industry played in New Zealand's international brand, he said.
The minister in charge, Primary Industries Minister Nathan Guy, would also be briefed today.
What the footage shows:
*Calves being born during mid-winter frosts with no shelter
*Distressed cows having their calves taken away from them shortly after birth
*Dead calves in piles at farm gates
*Live calves in crates on the side of the road with no shelter, food or water. This often occurred in extreme weather conditions and at times for more than eight hours, despite the law requiring them to be fed two hours before transportation.
*Truck drivers roughly throwing calves into the back of trucks
*A slaughterhouse worker kicking, hitting and throwing calves, before bludgeoning them and slitting their throats.