Peter Morris, NSA chief executive, vowed to fight against compulsory EID and said it was vital the industry highlighted the difficulties it would cause farmers.
His comments came after DEFRA minister Jane Kennedy conceded that the government would have no choice but to implement the legislation.
Mr Morris said he was disappointed the UK government was not “showing a little more fight” and compared Mrs Kennedy’s position with the more robust response of the Welsh Assembly Government rural affairs minister.
“Elin Jones has been much clearer in saying she didn’t want it to be introduced but that her hand is being forced,” Mr Morris said. “Jane Kennedy is telling us to face the inevitable.
“DEFRA says January 2010 is the date and the only question now is how it will be implemented.
“We shall continue to fight it but we are obviously in discussion with DEFRA over the planned implementation and highlighting any difficulties for farmers.”
Mr Morris said political pressure was being brought on the European Parliament and the industry was busy lobbying MEPs.
Welsh Liberal Democrat MP Mark Williams, who initiated a debate in Westminster over EID, said he had urged MEPs to keep up the pressure.
“The Minister accepted that the government would not implement this decision if they had a choice and assured us that they were continuing to make representations,” he added.
“It is now vital that we keep the pressure on the Commission to look at this matter again and give the UK a derogation from this regulation.
“There has been an excellent cross-party campaign on this issue and this must be continued if we are to have any chance of changing the Commission’s mind.”
A campaign has been launched to get more than half of all MEPs to sign the European Parliament’s written declaration against the plan so that it can be noted in the minutes as the Parliament’s position.