The introduction of electronic identification of sheep will cost the UK more than £65m, according to an economic analysis of the scheme.
Farms will carry 92% of the costs of introducing the scheme next year, while markets and collection centres will face 5% of the bill, analysis by EU's Joint Research Centre found.
The remaining costs will be picked up by abattoirs.
The report, presented to the Standing Committee on the Food Chain and Animal Health, compares the impact of five options for implementing EID, using electronic ear tags in UK and The Netherlands and ruminal boluses in Spain and Cyprus.
The UK's bill for tagging all animals born from next year and on-farm reading for movements from 2011 was £65.2m. This compared with £38.9m in Spain, £4.7m in The Netherlands and £1.07m in Cyprus.
In the UK equipment would account for almost half of the cost, tagging 38% and reading 13%.
But if full tagging without on-farm movement readings was implemented, the cost to the UK would more than halve to £31m.
Despite the costs, the report says EID generated benefits at farm level, for official controls and downstream in the production chain.
"When fully implemented it reduces the time needed for movement and tracing investigations," the report claims.
But the Farmers Union of Wales described the £109m cost of implementing EID in the four countries surveyed as totally staggering.
Derek Morgan, chairman of the union's hill farming committee and a member of the Welsh assembly's EID group, said the report demonstrated how heavily UK producers would be penalised.
"This is a cost that will not be borne by our competitors from outside the EU," he said.
"Once again it highlights the completely disproportional costs of implementing a technology that can have major technical problems associated with it.
"I dread to think what the full costs to the EU sheep industry will be when even the cheapest option, which involves market reporting rather than on-farm reporting, represents a cost of £31.024m for the UK alone."
The costs of EID were overwhelming while the benefits were negligible and could actually be negative during a disease outbreak," he added.
"We are committed to fighting against this ridiculous legislation to the bitter end and this analysis is yet more evidence that totally undermines the basis upon which the Council of Ministers has made its decisions."