The judgment, delivered on Thursday in an appeal taken by a farmer and two pharmacists against the Department of Agriculture, has opened a Pandora's box of repercussions which government advisers are frantically trying to shut again behind the scenes. It strikes out various indictable offences, including the use of dangerous growth-promoting drugs such as angel dust.

The ruling has left it open to people previously found guilty of such offences under the Animal Remedies Act 1993, some of whom were jailed for their activities, to have their convictions overturned and to claim compensation from the state.

Meanwhile, hundreds of ongoing prosecutions had been frozen pending the outcome of the appeal. In one case alone, the legal bill to date is estimated at 5m.

In a move reminiscent of the fall-out from the Mister A and CC statutory rape crisis last year, the Supreme Court is to hear legal submissions in the next law term on the fall-out from Thursday's judgment.

Though the appeal specifically related to the Animal Remedies Act, the finding that government ministers are not automatically entitled to create indictable offences by statutory instruments could have implications for hundreds of thousands of ministerial orders giving effect to EU regulations going back to Ireland's entry to the EEC in 1973.

The departments of agriculture, the marine and the environment, which routinely issue ministerial orders arising from EU law on farming, fishing and waste disposal, will be widely exposed to court challenges in the wake of the verdict. Several thousand legal instruments emanate annually from the EU, which is expected to impose punitive fines on Ireland for the legal mess.

An Oireachtas bill, designed to retrospectively close the loophole identified by the court, had only completed its committee stage of passage on Wednesday night. The European Communities Bill 2006 is due to be rubberstamped by the Seanad next week but legal sources are predicting that President Mary McAleese will have little choice but to refer it back to the Supreme Court.

"Aside altogether from Thursday's ruling, the bill is porous with loopholes, " believes a senior counsel who has read it. "It doesn't robustly enough retrospectively defend all European law transposed into Irish law with criminal sanction since 1973. It's undoubtedly open to challenge."

The European Communities Bill was introduced in the Seanad last November by junior foreign affairs minister Noel Treacy.

It will be salt in the wounds of taxpayers faced with footing the inevitable bill for EU fines on which the Supreme Court had already rung an alarm bell three years ago over Ireland's bungling transposition of EU law.

In that case, a Kerry fisherman charged with using a prohibited drift net for tuna fishing asked the Supreme Court to determine if the marine minister, John Browne, could create an indictable offence under the Fisheries (Consolidation) Act 1959. The court ruled in July 2003 that the minister did not hold such power.

As the Attorney General's advice to government is exempt from the Freedom of Information Act, it has not been possible to establish if ministers were warned after the 2003 case, Browne v the Attorney General & Others, that the orders they were signing were vulnerable to legal challenge.

The case that resulted in Thursday's judgement arose from the prosecution by the Department of Agriculture of a farmer and two Mayo pharmacists, a father and son, under the Animal Remedies Act. Trinity College law professor Gerard Hogan, who also acted in last year's statutory rape case, and barrister Randal Hill represented the appellants. Four senior officials of the department's Special Investigations Unit (SIU) left court without comment after the decision was delivered by Judge Susan Denham, who wondered, in her written judgment, if the loophole had arisesn from "a policy decision by the Oireachtas" or "an oversight in drafting".

According to legal sources, the verdict has raised a question about the validity of the SIU itself.