Green MEP Ms Nuala Ahern has complained to the Standing Committee of the Berne Convention and the EU over the killing of 1,300 badgers by the Department of Agriculture.
They were killed in an experiment to reduce levels of bovine TB. Ms Ahern said badgers are a protected species in Ireland.
The Department confirmed yesterday that it had applied for a licence to remove badgers in four areas, to validate the findings of a project in east Offaly.
The area covered by the licence is around 1,200 sq km and is in TB blackspot areas in Kilkenny, Donegal, Monaghan and north Cork.
"The number of badgers removed from these areas to date is some 1,300. Twenty one per cent of these were subsequently identified as having tuberculosis," it said.
"In the east Offaly project area, the number of reactor animals removed per year was running at 350 per annum prior to badger removal.
"Subsequently, this figure dropped to circa 50 per annum after four years and has remained at this level since," it added.
The statement concluded by saying that the four new project areas are not expected to show results for at least three years following badger removal.
But yesterday, Ms Ahern said that the badger was being scapegoated by the Department because of the poor management of the bovine TB eradication programme.
"The way the animals are being killed, mainly by snare, is totally unacceptable and is in breach of Appendix 11 of the Berne Convention," she said.
She added that she will also bring a complaint against the Government through the EU, because the badger is a protected species under the 1976 Wildlife Act.
A spokeswoman for Badger watch Ireland said yesterday that the figures released by the Department were horrifying and it would mount continuing opposition to the ongoing destruction of the species.
"The only figures we have would indicated that the badger population in Ireland could be as low as 150,000 and the extension of the licence to kill more of them is a disgrace," she said.
She said it was most likely that bovine TB levels had fallen in project areas because the farmers were being more closely monitored than previously and there was no conclusive evidence that badgers spread the disease.