The issue was under discussion at the meeting of the Council of Agricultural Ministers at the request of the Hungarian government, which called for EID tagging to be a voluntary rather than compulsory measure.
Farming union representatives flew to Brussels with Defra food and farming minister Jane Kennedy to lobby ministers and encourage them to abandon plans for compulsory EID tagging.
However, despite eight other countries coming out in support of the UK stance, Commissioner Androulla Vassiliou confirmed the regulation will come into force on December 31 2009.
NFU livestock board chairman Alistair Mackintosh, who was in Brussels for the meeting, said that dialogue will now continue with Defra in order to explore ways of reducing the implications of this regulation on sheep farmers.
He said: "We remain fundamentally opposed to the individual movement recording of sheep, but the Commission is still determined to start to implement this regulation from the end of this year.
"However, following these discussions, we believe the door is now open for further talks and we will work closely with Jane Kennedy to see what we can get from this."
Mackintosh added that while Commissioner Vassiliou made it clear that the proposals will go ahead, he indicated that there will be some flexibility regarding implementation.
"We are now working to ascertain how far this will go," he said.