The RSPCA has suspended three Freedom Food-accredited farms over allegations of animal neglect.
It is investigating after undercover film footage aired this week on ITV showed injured and diseased turkeys on a Norfolk farm that participates in the high welfare Freedom Food scheme.
The report on Tonight showed pigs on another Norfolk farm in soiled conditions and with no straw or dry area to rest.
A spokeswoman said: "We're shocked and frustrated about this."
But she rejected claims by an unnamed former RSPCA employee on the show that lapses were inevitable because Freedom Food only had 10 full-time inspectors. "They carry out more unannounced checks than any other assurance scheme in the UK," she claimed. "About 50% of our 2000 members, including farms, processors and hauliers, get spot checks every year."
The ethical food market is thought to be worth about £2bn and products bearing the Freedom Food logo, or claiming to be free range, retail at a premium to conventional meat.
NFU poultry board chairman Charles Bourns said he wasn't surprised about the revelations, but appealed for consumers to keep buying welfare-friendly food.
"It is not necessarily representative of the industry. Those pictured are just bad eggs. You'll find good and bad welfare in every system."
The key to good welfare was well-trained farm workers, he added. "Welfare is only as good as the man looking after the animals."
Freedom Food refused to confirm whether it had received enquiries about the footage from buyers. But it vowed to kick the farms out of its scheme if the accusations were verified. In the meantime, no animals were leaving the farms for slaughter.