Prime Minister John Key and Agriculture Minister David Carter yesterday joined growing opposition to "factory farming" in the Omarama-Ohau area.
They both cited fears of a negative impact on New Zealand's international free-range brand.
After heated debate on the issue in Parliament yesterday, Mr Key said "the Government doesn't support it".
"It might also be helpful to point out the National Animal Welfare Advisory Committee . . . has recently developed a dairy welfare code," he said.
"The code is yet to be finalised and published, but the Minister of Agriculture advised me he has asked for urgent advice on the specific issue in relation to that code."
Mr Carter said farmers had been contacting him with concerns about the proposals to establish 16 dairy farms using cubicle stables to house up to 17,850 cows.
They were aware of the potential danger to New Zealand's reputation, including all of its primary producers, "if this goes wrong", Mr Carter said when contacted yesterday.
Mr Carter said he would be keeping a close eye on the issue and had asked for more information from the Ministry of Agriculture and Forestry about how cubicles stables worked.
Mr Carter also said he had a concern about intensive dairy farming in the area because of its fragile environment.
The Green Party urged Mr Key to "show leadership" to protect New Zealand's reputation and export industries from being damaged.
In a statement, co-leader Russel Norman, who has described the proposals as "factory farming", said the Government should use its power under the Resource Management Act to "call in" what was obviously a matter of national significance.
In Parliament, Mr Key said he shared the concerns of Fonterra and the Green Party that factory farming was a threat to New Zealand's reputation.
When contacted yesterday, Richard Peacocke, a director of Williamson Holdings and Southdown Holdings - two of the three companies making the resource consent applications - said he was "not talking to the press".