"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.
A SAFE investigator said he wanted to expose what went on in farms, rather than to hurt farmers.
"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.
Hans Kriek, executive director of the animal rights organisation, 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.
"So a complaint was made to MPI and to date we have not heard back from them. This is now about two months ago."
Matt Stone, from the Ministry for Primary Industries, 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 farm 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.
