The proposed revisions to the IPPC measures include reducing the current thresholds from 40,000 to 30,000 for laying hens, 24,000 for ducks and 11,500 for turkeys.
This would mean smaller free-range and organic poultry farms would be included and increase costs to a sector already burdened with rapidly rising feed and fuel bills.
In addition, a new provision which would extend the measures relating to the spreading of pig and poultry manures to manures spread by third parties.
NFU poultry board chairman Charles Bourns said he feared the increases in administration and costs incurred by some seasonal producers if the proposals got the go ahead could be the last straw for some smaller farms.
“At a time when turkey production is already declining, yet consumer demand for home-reared birds is on the up, it seems madness to be increasing thresholds which could see many small producers, including free-range and organic, going out of business,” he said.
“Extending IPPC controls to third-party spreading of manures would be costly and jeopardise arrangements between neighbours.
“We have been lobbying hard in Brussels to influence the discussions taking place in the EU Commission about the proposals and will continue our efforts to get them changed,” said Mr Bourns.