The Ministry for Primary Industries is being accused of handing out misleading information to farmers at a Mycoplasma bovis meeting.
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The disagreement revolves around the Privacy Act and farmers' frustrations at not being told the names of those with infected properties.
MPI's head of Biosecurity Roger Smith last week told 200 North Canterbury farmers the agency was prevented from naming them due to the Act, and doing so could result in it being charged.
Mr Smith made the comments at a meeting in Cheviot, one of a number MPI are holding around the country to keep farmers informed about the effort to eradicate the disease.
Mr Smith said MPI was as frustrated as the farmers were about the limitations imposed on it by the Privacy Act.
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"I've had three legal opinions, including from the Privacy Commissioner, who says that if we name a farmer, we're in a serious breach, and therefore we will be charged with an offence."
Mr Smith gave the farmers this advice if they were not happy with the Privacy Act: "I know you might think the law is stupid. The opportunity to change the law is to work with your local MP - unfortunately it's not an MPI law - it's a national law for this country...our hands are bound."
It comes after MPI accused farmers of not cooperating and making the job of handling the disease harder.
However, Privacy Commissioner John Edwards said farmers had been misled by MPI on this.
"The most charitable construction I could put on that excerpt is that he's just got completely the wrong end of the stick. We have not given a legal opinion to that effect.
"But there is no possibility of being charged in terms of a Privacy Act breach. As I say, the law that applies in relation to this matter is primarily the Biosecurity Act."
Mr Edwards said he had been in contact with MPI and it was now working on amending what it said to farmers around the Privacy Act to ensure they were being given accurate information.
In some circumstances MPI did have the power to name those with infected properties, he said, but it needed to have a good reason why and it must be necessary in helping it to control the spread of Mycoplasma bovis.
"You know we could say 'everyday in the newspaper let's have a new list of farms that are being tested' - would that be in the interests of the industry?
"It's possibly going to be disproportionate - it's going to be an over disclosure of information that doesn't serve any biosecurity need."
Mr Edwards said naming those with infected properties could make it more difficult to control the spread of the disease by dissuading others from coming forward for fear they might be named and shamed.
You can hear more on Insight's investigation into Mycoplasma bovis and farmer's frustrations on Sunday Morning.