The Department of Agriculture and Food's animal-feed sampling and testing regime, under which it has seized hundreds of tonnes of imported animal feedstuffs, has been found by the High Court to be faulty.
The ruling has thrown into doubt the system of checking used by the department, which it claimed is being used across the EU.
A department spokesman confirmed last night that it would be appealing to the Supreme Court the ruling of Mr Justice Peter Kelly in a challenge by importers Albatros Feeds against it and the State for impounding a consignment of animal feed from the United States in November/December last year.
He ruled that the tests carried out, which found samples of bone in the feed, did not prove that the presence of bone fragments indicated processed animal protein.
Irish regulations are based on EU legislation introduced in the early 1990s banning any bone material in cattle feed. It has been used extensively in the last decade as Ireland operates a zero-tolerance attitude towards any bone material found in cattle feed.
Samples of the maize gluten, which formed the basis of the case, were discharged at Foynes and Ringaskiddy and were found to contain particles of bone known as "spitule" when tests were carried out on the them abroad.
However, on Monday in the High Court, Albatros Feeds challenged the seizure of more than 7,400 tonnes of the material, which is normally incorporated into animal feed.
It claimed the authorised officer did not have the necessary powers under the Irish legislation to impound the feed and instruct its recall from the market. It also claimed that the Minister could not prove that the presence of bone fragments indicated processed animal protein.
Mr Justice Kelly found for the appellant on both issues, ruling that the department official did not have the necessary power to seize the material and instruct its recall from the market.
However, of greater significance was his ruling on the second issue, which rendered useless the system of testing for processed animal protein used by the department for the last 15 years.
The incorporation of meat and bone meal into cattle feed has been banned by the EU since 1989 and was banned from pig and poultry rations in 2000.