The lobby group yesterday defended itself in response to an anonymous letter from a Southland vet to Mr Carter, claiming the federation was defending a Southland dairy farmer over one of the worst cases of "systemic animal neglect and mismanagement", the vet had seen in 20 years.
In June this year, the federation complained to Mr Carter about the "bullying and intimidatory behaviour" of Ministry of Agriculture and Forestry (Maf) staff who visited 20 Southland farms despite there having been no animal welfare complaints.
Mr Carter ordered an investigation into Maf's conduct, with the report due within the next month.
But a letter to Mr Carter from a Southland vet sent in August, and released to The Southland Times after an Official Information Act request, has reignited the debate, with the unnamed vet calling the federation "reprehensible" for defending a Southland dairy farmer.
Federated Farmers board member and Southland farmer David Rose angrily rejected the criticism, saying the issue was not one of animal welfare, but the way Maf conducted themselves on farms.
"This isn't about animal welfare; this is about the way it was handled."
At the time, it was alleged Maf staff arrived unannounced, intimidated farm workers and ordered staff out of dairy sheds during milking.
So far, there has been no prosecutions stemming from the visits and farmers said in June, based on their experience and knowledge of farms visited, there were no animal welfare concerns.
In response to a request from Mr Carter, Federated Farmers collected confidential statements from 16 Southland farmers who were visited by Maf, but the release of the vet's letter has led Mr Rose to question the process.
The investigation was incomplete, and Maf and the federation had a written confidentiality agreement to ensure the free flow of information about the allegations, Mr Rose said.
"We expected the report to be the next thing they would deal with," he said.