Maheno farmer Kerry Dwyer fears animal welfare issues will arise if cattle on properties under restricted place notices due to Mycoplasma bovis are not slaughtered.
The Ministry for Primary Industries will cull 22,332 cattle, after it was confirmed the disease was not endemic.
That comprised 11,842 cattle on 10 properties in Southland, 1275 on a Middlemarch property, 5952 on six properties in the Waimate and Waitaki districts, 3253 on four properties at Ashburton, and 10 cattle on a Canterbury property.
Only confirmed infected properties (IPs) were being directed to cull their herds.
Properties under restricted place notices (RPNs) - of which there were 48 - or notices of direction (NoDs) would not be directed to cull.
Mr Dwyer and his wife Rosie, who bought calves from the affected Van Leeuwen Dairy Group, voluntarily sent 400 calves to slaughter, against the advice of MPI, but they felt they had no choice.
Yesterday, Mr Dwyer said if animals on RPN properties were not slaughtered, farmers would end up with animal welfare issues as the animals could not be moved without MPI approval.
Read more: 'Dark moments' dealing with Mycoplasma bovis
They would become overstocked, having not enough feed, which would lead to stressing the animals which would then lead to the disease becoming symptomatic and cattle becoming sick and dying.
''That has already happened on some properties. So, unless MPI give up trying to stop the bug, the only sensible option for those farmers is to have the animals slaughtered to pre-empt animal welfare issues,'' he said.
MPI said it would help farmers under RPN and NoD notices to develop ''tailored management plans to carry them through this short period of uncertainty''.
When contacted, Federated Farmers dairy industry group chairman Chris Lewis agreed the concerns raised by Mr Dwyer were a ''real risk''.
Testing needed to be sped up so farmers could return to routine as quickly as possible.
The situations some were in were ''unimaginable''.
There must also be a speedy resolution to compensation payments so farmers could get normality back into their businesses, Mr Lewis said.
It was also very important to give bankers and other parties assurances they had money coming.
At the moment, some did not know whether they were getting paid.
Anyone struggling with feed shortages should contact MPI immediately to ask for assistance to buy in feed and that should be actioned quickly, he said.
MPI's director of response Geoff Gwyn was travelling yesterday and unavailable to comment but he would respond today, an MPI spokeswoman said.