The Minister said he wants to see vaccinations for badgers introduced "sooner rather than later". He was speaking in the Dáil in response to Independent TD Maureen O'Sullivan.
"I am confident [that culling] can be replaced by a badger vaccination programme in due course and, as far as I am concerned, the sooner the better but I need to do it on the basis of science," he said.
"It would be dishonest of me to say that I do not think that the badger targeted cull programme is being done in as humane a way as we can do it," he added.
The TB eradication programme has resulted in a fall in reactors over the years, despite a slight rise in 2014. In 2005, 25,884 cattle tested positive for bovine TB. Ten years on, the figure is 16,145 – down 38%.
Despite the link between badgers and TB, the results of a recent study by the Agri-Food and Biosciences Institute (AFBI) in Northern Ireland has suggested that it is unlikely that direct contact between badgers and cattle is a major factor in the spread of the disease.
However, Minister Coveney defended the current programme.
"If there are other suggestions as to how we can do it better, we would happily take them on board but to suggest it is not working would be wrong," he said.
"The incidence of TB in cattle has fallen by almost 40% since 2008 and is currently at record low levels. It is particularly interesting that the incidence of TB in Northern Ireland, where badger removal is not prioritised, is approximately twice as high as on this side of the Border," he said.
"[The eradication programme] is based on a number of studies which showed that badger removal had a significant beneficial impact on the risk of future breakdowns, with areas where badgers were not removed being some 14 times at greater risk than in areas where badgers were removed."
The priority is to remove TB from the Irish herd, even if that involves the culling of animals, the Minister added.
"We want to stop killing animals because they are carrying or spreading TB. The way to do that is to eradicate TB, which is what we are trying to do. That is in the welfare interests of animals as well as the interests of farming," the Minister concluded.
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