Where a farm was directed to cull its stock, compensation and support would be provided accordingly, it said.
Mr Wheeler and his wife Jan, who farm near Moeraki, "never had the disease from day one", he said.
Their farm was put in lock-down because it was a tracer property from Kerry and Rosie Dwyer who bought calves from Van Leeuwen Dairy Group, the first property in New Zealand where the disease was detected.
The Dwyers' property, at Maheno, was confirmed as having Mycoplasma bovis in August last year.
Mr and Mrs Wheeler's farm was placed under a notice of direction that same month and it was effectively in "major lock-down".
Their cattle were tested; some four times, some several times, some once, and all returned negative tests. Each test cost about $400, he said.
MPI decided to kill their yearling cattle and Mr Wheeler said they were verbally told by someone from MPI that she believed they would get the value of those cattle the same as when they would have usually killed them.
Mr Wheeler weighed every animal and before it was trucked to slaughter and recorded it with its tag number. He received just under $100 for each animal from Oamaru Meats.
Mr Wheeler was then told, after the stock had gone, that the cattle would be valued by a person from a rural services company.
He said that was "hardly fair", given that person did not have the weights, or have any knowledge about the farm or situation.
Mr Wheeler went to the Temuka stock sale that week and made his own valuations based on the prices of cattle of the same weights as his.
His compensation claim was solely for the value of his animals; there was no account for time or loss of income; it did include the difference between what he killed 20 heifers for and what he was going to get from a stud farmer who was purchasing them for embryo transplants, but had to call the deal off.
When the offer came back, one-third had been cut off it and it would not be enough to replace the animals, he said.
"What concerns me most is that you can't take their word. You have to get something in writing. I think we've got to make a stand," he said.
He had been "'on the case", not only to MPI but also he had sent emails to Agriculture and Biosecurity Minister Damien O'Connor, and Prime Minister Jacinda Ardern.
He asked Ms Ardern a month ago if she would be available to meet a group of farmers during her brief visit to Oamaru on Thursday to discuss their problems with claims but did not get a response.
Mr Wheeler responded to the compensation offer by saying he was not happy with it and he would probably take it to arbitration.
He heard back that he could be paid the money offered and then go on further to arbitration and court if he had to.
He emailed MPI saying he wanted that in writing, that if he took the offer it would not be detrimental to him if he followed up with arbitration, and he wanted the bottom of his claim to be signed by MPI director-general Martyn Dunne. He had not heard back.
The compensation that he sought was going to buy his income for next year; he did not have that money until he could get the claim sorted, and he went for five months without any income.
Mr Wheeler was also critical of MPI's communications and handling of the response, citing the example that when MPI first arrived on his farm, they thought he had herringbone and rotary dairy sheds, despite being a drystock sheep and beef farmer.
"It's ... unbelievable. It's been an interesting exercise, to say the least," he said.
"It's been a straightforward claim. I can't see why they are stuffing me around," he said.
Mr and Mrs Dwyer remained in regular contact with them and others that bought calves, and it was good to have that support among the group.
Mr Wheeler was frustrated that they "did everything by the book" as far as their response to the disease, including contacting neighbours immediately and telling them to keep their stock away from boundary fences, and ringing contractors and suppliers to tell them to stay away, and yet the way they had been treated was "quite appalling".
Those preparing to have their stock slaughtered needed to know that it did not matter how much they helped MPI out, they were not going to be treated any better.
"It's quite important to put a peg in the ground and say how we're being treated. These guys should be very wary. Don't take MPI's word for granted. They want to get stuff in writing."
Mr Dwyer, who has previously expressed concerns about the compensation process and MPI's handling of the disease response, said their group — he and his wife and a wider group of 18 farms — sent 10 claims to MPI over January and February and have had only several offers back.
The Biosecurity Act stated they should be no better off and no worse off due to MPI exercise of powers — all the group were worse off because they had spent a huge amount of time and energy dealing with MPI, without having infected animals — apart from Mr and Mrs Dwyer and their son Tom, he said.
"They have had their businesses disrupted physically and financially, which will take years to rebuild. They have business and personal relationships stressed or destroyed. None of these things qualify as 'verifiable losses' under Biosecurity Act Terms," Mr Dwyer said.
Personally, and as a group, the farmers were "very very frustrated" by MPI indecision, lack of attention and reply and conversation.
"They make the rules but won't tell us what the rules are and they change the rules," he said.
MPI director of response Geoff Gwyn said MPI was committed to supporting affected farmers to get their due compensation and get back on their feet as soon as possible.
"Together with stakeholder organisations such as DairyNZ we are working with farmers to guide them through the compensation process so they're aware of what is specifically needed to ensure any claim for compensation is dealt with efficiently. As part of this, we are boosting our compensation team to process claims as soon as we can so farmers aren't out of pocket for longer than they need to be.
"However we acknowledge that at times the process can become complex and time consuming, but when public money is at stake we will take every step necessary to fairly administrate the compensation scheme," Mr Gwyn said.
Compensation payments for culled cattle were based on market valuations carried out by an independent valuer, and receiving a compensation payment did not prevent a farmer from requesting a review of that payment. Claimants could request MPI reviews the compensation amount, and there was a process for them to do so, he said.
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