Mr Hay recently emailed Prime Minister Jacinda Ardern to highlight the effects M. bovis had on their business.
He questioned how many other farming lives would be "destroyed" during the eradication process.
"The decision to eradicate M. bovis was made and a lot of money invested to do so. From what I see the majority of this is to run the eradication process, with compensation for those who need it difficult and drawn out, but the worst thing that I think is being overlooked is the human cost.
"Is the human cost going to be worth it and, if so, why aren't the affected being looked after properly?" he said.
Mr and Mrs Hay, who had a dairy grazing business, have been affected by M. bovis for the past 17 months.
When one of their three graziers had a positive test for the disease, their own property was placed under a notice of direction in December, 2017.
After three months of testing, they were cleared of having the disease and left to try to restart their business.
But that was not possible due to the timing and availability of stock for that type of business, Mr Hay said.
The only option was to buy stock to finish, which they did from April to mid-June. That was their third year after an extensive irrigation development, so they had never budgeted on borrowing more money to buy stock - they had budgeted on grazing other people's stock.
Geoff Gwyn
It was difficult to get finance. The bank was not interested and they were not able to get enough stock to be comparable to their previous grazing position.
In mid-August last year, they were told they had 21 trace animals to M. bovis. After three months of testing, they were told they were clear of M. bovis but "in the next sentence" were told they had four more trace animals.
As a result of that, they were made a restricted property and were in the process of depopulating 745 animals.
Because of the irrigation development, it had put Mr and Mrs Hay in an "impossible position".
Mr Hay was one of the drivers of Haka Valley Irrigation Ltd, a small group of farmers who brought water to the traditionally dry valley.
His grandfather started irrigating in 1921 and the development of irrigation over the generations was a natural progression.
It was now fully irrigated, which had taken about 20 years to get through the investigation, consents and finally construction process.
Mr Hay acknowledged the couple were under financial pressure - "we're not trying to run away from that" - and they had gone through the development process with their "eyes open", knowing the risks. But they still believed they could have worked their way through that.
They had been pushing up numbers for grazing and "all of a sudden that stopped". The last 17 months had been spent "just going backwards".
"I was at a meeting in Ashburton some time ago and told we, the affected farmers, are `taking one for the team', that the industry benefit will far outweigh our losses and we [the affected] are, on the whole, only a small percentage of the total agricultural industry.
"I came away thinking I have never played in a team where we leave any team members behind, but in this case it seems so.
"At another meeting I attended, affected farmers were scared to speak out publicly about the effects M. bovis is having on their businesses, with the concern that they get penalised through the compensation process if they do.
"Because they don't speak out and reporting about the direct effect on farmers isn't done, a skewed picture is created.
"This picture, I fear, leads to the assumption that everything is fine within the farming community when, in reality, families like ours are having to sell up, losing their business, income and home."
Compensation did not cover the true cost associated with the effects of M. bovis to the farmer.
"We keep getting chucked back in our face what legislation won't allow Government to compensate for in this situation. Our Government has recently shown that they can change legislation within a very short time, when there is a collective will.
"Why hasn't our industry pushed harder for legislative changes, to support those affected by government-enforced restrictions due to M. bovis, rather than a proposed time-consuming review of the legislation?"
Many people had worked very hard for them in the Ministry for Primary Industries - and others had "gone beyond what we could ever expect or wish for" - especially now, as it was clear theirs was one of the more badly affected properties.
"But their frustrations are ever present about the processes they have to deal with while trying to help us.
"Most farmers just want to get on with their normal business but M. bovis has changed everything and being tied up in this process, I think, is more concerning for the individual farmer than the disease.
He acknowledged MPI had "stepped up" in latter times and was doing more for affected people's welfare.
He hoped by highlighting their situation that other farmers who were affected would speak out to share their experiences and effects of M. bovis. "Otherwise nothing will change and the pain will continue".
When asked for comment on Mr and Mrs Hay's situation, Mycoplasma bovis programme director Geoff Gwyn said being out of business was the "worst possible outcome" and the last thing MPI wanted to happen.
MPI had worked "long and hard" with the couple and he had meetings with them. He believed MPI had done everything it could to support them.
He believed the Hays had faced challenges in their business model and M. bovis "hasn't helped".
Other farmers had spoken publicly about the effects on their businesses and that was "absolutely the right thing to do". Not one had been penalised for doing that, he said.
Attending farmer and public meetings throughout the country last week, Mr Gwyn said the angst was still there, as would be expected.
"We're better than we were a year ago, which is cold comfort I know for those there a year ago."
There were a "huge" number of people working for him, including industry partners, who wanted the eradication programme to be successful and wanted to minimise impacts on people.
"I wake up in the middle of the night worrying about some of these farmers. All my people are working their damndest to get the best possible outcome for farmers."
