All horses and ponies in the UK will need a new passport
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The government has admitted the proportion of the UK's horse owners applying for 'passports' for their animals could be as low as 50%.
By the end of February all horses, ponies and donkeys in the UK must have a passport booklet.
The system is designed to show that horses exported to Europe are free from dangerous veterinary drugs.
Rural Affair Minister Alun Michael told the BBC compliance is between 50 and 80%. Owners face fines of up to £1,000.
The situation has been further complicated by the fact that because horses are not considered farm animals, no formal record of their numbers is kept, said Mark Holdstock of BBC Radio Four's Farming Today programme.
The total number of horses and ponies in Great Britain is estimated at between 600,000 and just under 1m.
After 28 February 2005, animals without a passport cannot be sold or exported, moved from one place to another or slaughtered for human consumption.
Nearly 500,000 of the documents have so far been issued by the government.
Food chain risk
The basic purpose of the European regulations is to prevent horses entering the food chain if they have been treated with certain veterinary medicines.
Rural Affairs Minister Alun Michael said obtaining a passport without delay was "in the best interests" of horse owners who had not yet complied.
"A key concern for government and for the horse industry is that approval for around 60% of UK veterinary medicines could be withdrawn if the European Commission is not satisfied with compliance.
"Many of these are commonly used and are relied on by horse owners. Their withdrawal could have important welfare implications."
He said enforcement would be "proportionate and fair" and in the first instance focused on key hazard points, such as slaughter houses and export points.