Equine charities in the South West have raised concerns that new horse passports, which could soon become law, could lead to animals being dumped or shipped abroad.
The new regulations take effect from next year
The document, which donkeys will also require, would list the animal's history and show if it has been treated with veterinary drugs.
If that is the case the animals cannot legally be incorporated into the food chain and disposed of by an abattoir.
Maureen Rolls from South West Equine Protection is concerned by the move.
"If an animal has had any treatment at all then obviously they are unfit to go for slaughter," she said.
"If that stops then obviously we have a problem with wild moorland ponies, where they are going to end up, and my one dread fear is that these animals are going to go to the continent alive."
The Devon-based Donkey Sanctuary, which looks after more than 5,000 donkeys, says it faces a bill of £30,000 for the passports and associated administration even though none of their animals will ever enter the food chain.
But others believe the new rules could have benefits, including a reduced risk of buying a stolen horse.
Details of all horses issued with passports will be recorded on a proposed National Equine Database, benefiting breeding programmes and research.
"I think the horse passport system is a good idea because horses are going to be identifiable," said Devon vet Sarah Taylor.
"They are going to be traceable and we are going to retain the right to use drugs that are effective without any risk to the human food chain."
The documents were due to be compulsory from January but their implementation has been put back six months.
The only exemption will be Dartmoor, Exmoor and New Forest ponies but even they will need passports as soon as they move off the moorland.
The changes have come about as a result of an EU directive.