MPI previously pleaded guilty to two charges of exposing individuals to risk or harm or illness following a prosecution from WorkSafe.
Co-offenders in the case AsureQuality Limited and OneStaff (Queenstown/Invercargill) Limited were sentenced last year.
At the time, AsureQuality was fined $66,000 plus court costs of $2392.93, while OneStaff had to pay $38,500 and the same amount of court costs.
Both were also ordered to $1666.66 each with each of the five workers receiving $1000.
At the hearing today, Worksafe prosecutor Katie Hogan said MPI engaged Assure Quality to deliver cleaning and disinfection as part of the response to Mycoplasma bovis.
She said MPI was the Government agency which had the responsibility for the response, and it had breached ''the primary duty'' to ensure the healthy and safety of its workers.
It had failed to co-ordinate, monitor and identify the risks and the appropriate controls, such as the use of personal protective equipment and training, at the farm.
MPI representatives were in Invercargill at the time and were holding daily briefs, so the incident could have been avoided, she said.
Hogan submitted the culpability of MPI was lower than AssureQuality but was greater than One Staff — as the second company did not have access to the farm where the cleaning process was taking place.
Defence counsel Chris White said MPI was disappointed to be in court as it took the health and safety of its workers ''very seriously'' and considered itself a leader in the matter.
He said it was the first time MPI had ever been prosecuted on health and safety charges and it had identified and implemented a number of changes following the incident.
White submitted MPI had a lower culpability than the other parties as it did not have a ''hands on'' role, controlling the day-to-day operations.
However, he acknowledged MPI could have done more to ensure AsureQuality Limited was following its safety plan.
''If the safety plan had been followed, we would not be here.''
Judge Russell Walker agreed the culpability of MPI was lower than the other co-offenders and acknowledged the ''previous good character'' of the Ministry.
He ordered MPI to pay $30,000 plus prosecution costs of $3800 and pay $1666.66 in reparation for the five workers - a third of the total $5000 reparation payment.