The Irish Cattle and Sheep Farmers' Association (ICSA) has said that questions need to be answered in relation to the handling of animal welfare cases by the Department of Agriculture, Food and the Marine (DAFM).
In recent days, videos have been attracting attention and shared widely across social media allegedly showing less than best practice in an official culling of animals on a farm.
ICSA Animal Health and Welfare chair John Barron said: "ICSA is not commenting on the individual case, which is before the courts.
"Allegations of animal welfare breaches are extremely serious and must be dealt with through the proper legal process.
"However, there are important questions that need to be answered about how enforcement interventions of this nature are carried out."
He explained that the images that have emerged have caused "considerable concern" across the farming community.
The ICSA chair urged that in any circumstance where animals have to be euthanised, it must be carried out in a humane, professional and controlled manner that minimises suffering and unnecessary distress to the animals.
"If there are lessons to be learned from how these interventions were planned or executed, they should be identified quickly so that any future actions are carried out in a way that avoids unnecessary distress for both animals and those present," Barron said.
He added that DAFM has "extensive enforcement powers" and that these powers come with "a responsibility to ensure those powers are exercised to the highest standards".
"Farmers are entitled to know exactly how these operations were carried out and whether the department's own procedures were followed at every stage."
The ICSA has outlined that where animals are subject to enforcement action, farmers need confidence that all appropriate options have been explored before a decision is made to euthanise them.
"Where alternatives are available, such as DNA testing or retaining animals under appropriate controls and continuing to feed them while further investigations are carried out, these should be fully assessed before any irreversible decision is taken," Barron said.
He emphasised that this is not about questioning the department's right to intervene when animal welfare requires it.
"It is about ensuring that, when these powers are exercised, they are used in a fair, proportionate and transparent manner that maintains confidence among farmers and the wider public," he said.
Separately, independent TD Mattie McGrath has said that DAFM officials must be "held accountable" to the same standards as farmers when it comes to animal welfare.
The Tipperary TD said the online footage has “shocked” rural communities, and has called on Minister for Agriculture, Food and the Marine, Martin Heydon to address the issue.
The Irish Farmers' Association (IFA) has also called for an urgent meeting with DAFM to discuss welfare and traceability protocols.
Agriland is awaiting a response from DAFM in relation to its protocol for carrying out enforcement action relating to animal welfare.