The committee heard that officials had been working with the farmer after “numerous” inspections, beginning in 2022.
The agriculture minister Andrew Muir said those had revealed a “grotesque” situation and “a large number of animals were caused unnecessary suffering”, leading to the deprivation order.
“That order legally required the department to deprive the individual of any livestock.
“The department had no choice.
“And so my officials took the necessary steps to fulfil this legal obligation.”
It emerged that a total of 21 animals had been removed during the grace period, but 51 remained on the farm.
Officials said animals in two of the areas on the farm were disposed of by 13:30 on 29 June.
The human slaughter operation in the final area was stopped when a local farmer offered to buy some of the remaining cattle.
But the animals could not be rounded up, and escaped onto the road.
They were eventually herded back and a vet recommended they be shot.
One remaining animal was disposed of on 30 June.
The carcasses were removed later that day.
Questions have been asked about the weapons used, the amount of ammunition, and why slaughter in situ was chosen as the method of disposal.
Deputy Chief Veterinary Officer Gemma Daly described the cattle as “semi-feral” and said staff had expressed concerns over the years about how to handle the animals without causing them stress, or risking injury to themselves.
Senior Principal Veterinary Officer Elsie McGarvey said the department was “technically” potentially in breach of the court order by extending the grace period.
She added that approximately half of the animals were not suitable for the food chain and others were too young.
And she said officials were “always prepared” that the farmer would be disqualified and they “knew” removing the animals would present “significant issues”.