A cull of 51 cattle in fields near Fivemiletown in June was lawful and appropriate, but operational shortcomings existed, according to an independent review.
The report found that there was insufficient thought given, when planning the operation, to the visual and emotional upset felt by people who saw carcasses lying overnight exposed in open fields.
Ireland's former chief veterinary officer Dr Martin Blake carried out a review of the operation.
The Agriculture Minister Andrew Muir said the reports findings are "accepted in full with regular reporting and independent oversight put in place to ensure improvements are driven and sustained at pace".
The cull was was undertaken after a farmer was found guilty of animal welfare offences and ordered to dispose of his livestock.
The review was ordered by the agriculture minister following complaints from politicians and farmers over how it was carried out.
The cull led to an emergency committee meeting at Stormont and a protest, with calls for the Minister Andrew Muir to resign amid a vote of no confidence by farming leaders.
Muir told the assembly he will publish an action plan on the review's findings.
The Ulster Farmers' Union (UFU) said the review "has exposed serious failures in governance, oversight and decision-making within the Department of Agriculture, Environment and Rural Affairs".
It added the review "identifies significant shortcomings in the planning, oversight and management of the operation, raising fundamental questions about departmental decision-making and the safeguards in place during major enforcement actions".
UFU president John McLenaghan said that while the union acknowledges the findings "regarding the legal basis for the operation and the method of culling, its wider conclusions make for deeply concerning reading".
What happened in Fivemiletown?
In May, a court ordered that the farmer be deprived of his animals when he was found guilty of animal welfare offences - they included 13 charges of failure to dispose of an animal carcass and six charges of causing unnecessary suffering to an animal.
He had a statutory two-week period to appeal, with the Department of Agriculture, Environment and Rural Affairs (Daera) giving him an extra week to make arrangements.
When the Humane Slaughter Team and departmental officials arrived to implement the court order, the farmer had made arrangements for 15 animals to be sold, but 51 animals remained on the farm, spread across three sites.
Most of the animals, on two of the sites, were culled by 13:30 BST.
When the operation began at the third site, some members of the public witnessed it.
That lead to a protest and a pause in the operation.
Another farmer arrived, offering to buy the animals, but they escaped on to the road.
After they were returned to the field, a vet who had been called to the scene said they were distressed and that the operation had to finish.
It was complete by 21:45.
The carcasses were removed by a specialist contractor the following day.
Blake review findings
During his review, Blake interviewed those involved in the operation, invited e-mail submissions from anyone who may have witnessed it, and had access to all paperwork and documentation.
His findings included:
Muir did not 'authorise or direct' operation
Following the report's publication, Muir said that "whilst the review finds that the operation was lawful, appropriate and sadly necessary from an animal welfare perspective, it's clear that operational shortcomings existed and planning gave insufficient consideration to the human and community impact".
"As minister I did not authorise or direct the operation," Muir said.
"When I then saw the distressing photos and videos of animal carcases and learned of the range of allegations that were circulating, I shared the genuine concerns expressed," he said.
He added: "That is why I moved quickly to order a full independent external review of the case. I would like to thank Dr Blake for his thorough and professional approach in conducting this review."
He said the report's 10 recommendations are "accepted in full with regular reporting and independent oversight put in place to ensure improvements are driven and sustained at pace".
Sinn Féin councillor Eugene McConnell first raised the issue of the cull at a Mid Ulster council meeting in July.
He welcomed the recommendations and urged the agriculture minister to fully implement them.
"DAERA have had to recognise serious shortcomings took place, and those lessons must now be acted upon in full," he said.
From the outset McConnell said his major concern was "the concerns of local residents and farming families" and that the department should have taken "greater consideration" of them.
"Going forward, the focus must be on ensuring that necessary animal health and animal welfare interventions are delivered effectively", he added.
Democratic Unionist Party (DUP) assembly member Deborah Erskine called the report "damning".
"The community was told to wait for this report to come out and see in the cold light of day what actually happened, actually what has come out in this report is exactly what the community were saying."
She added that Muir needs to "apologise".
Dr Blake recommendations
The review made 10 recommendations including changes to:
The Aera committee will hear from the permanent secretary and the chief veterinary officer in its regular meeting later this week.
There was criticism that neither Katrina Godfrey or Brian Dooher appeared at the emergency meeting in August.
The minister said that was due to personal reasons, and the officials who did appear had been directly involved in the operation.
