A public inquiry into the Ministry for Primary Industries (MPI) is being called for over its handling of the Mycoplasma bovis eradication.
Newshub has been leaked a letter from distressed farmers describing it as chaotic, stressful and slow.
Paul Tocker, spokesman for the first farmers to identify the bug in New Zealand, says they've only been paid half of their compensation claims.
"It needs to come out in the light of day because it's going to cost our industry - in fact, many of our industries - millions and millions more than they think it's going to cost, to try and eradicate. It's a nightmare."
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Mr Tocker says the van Leeuwen farm's owners are owed $4 million, and the ministry's handling needs to be looked at closely.
"The whole process that's been run, how this is being treated, how the decision to cull was made, how the decision for New Zealand to tray and eradicate was made - all that needs to be questioned," he told Newshub.
"Somewhere there are decision-makers or processes that they can't manage… I can't see any reason why they're suddenly going to start running it well from now on."
While Primary Industries Minister Damien O'Connor told Newshub he agreed many of the issues raised in the letter were legitimate, MPI's director of response Geoff Gwyn apparently dismissed the letter and called it a "shit-o-gram" according to Michael Salvesen, the president of Mid-Canterbury Federated Farmers.
MPI acknowledged the response to the outbreak hadn't been swift enough and apologised for any distress caused to farmers - but it stood by its compensation process.
Mr O'Connor said the eradication process was "on track".