At present, small abattoirs are charged an average amount for each animal inspected, rather than a full veterinary fee, which can be around £90 an hour.
Large abattoirs, which can handle 60 animals in an hour, can absorb such fees; but a small abattoir may slaughter as few as 30 or 40 animals over a week.
The FPB's food adviser, Bob Salmon, said: "There may only be just over 230 small abattoirs left, but 60,000 farm and catering businesses depend on them. Big abattoirs simply don't want to handle small numbers of animals."
He also pointed out that small abattoirs were major suppliers of halal and kosher meat. As well as criticising the proposed increase in charges, Salmon claimed that there is no need to have veterinary surgeons in small abattoirs all the time.
He argued that when a new inspection system was set up after the BSE crisis, Whitehall wrongly interpreted an EU regulation as meaning that a qualified veterinary surgeon should inspect animals and carcases in abattoirs.
This has meant the hiring of many foreign vets, often with limited English language and veterinary experience. Salmon said he knew of an abattoir where a Spanish vet sat in an office all day and "simply signed the forms put in front of her".
"There are highly qualified meat inspectors in every abattoir, who are quite capable of carrying out all the necessary inspection tasks," Salmon said. "We don't need veterinary surgeons to be present as well."