John O’Connor, aged 53, and Christopher McCarthy, aged 29, both of Kilbaha, Moyvane, Co Kerry, are charged with unauthorised turf-cutting on a designated area of conservation, Moanveanlagh Bog, outside Listowel.
They are due before Kerry Circuit Court for allegedly extracting turf without authorisation.
If found guilty, they face a maximum jail sentence of three years and/or a fine up to €500,000.
The offence with which the men are charged, the court heard, was created in September 2011 by way of ministerial regulations, which transposed the regulations into Irish law. It is their case it was not within the powers of the minister to create the offence in question in the manner done.
The appeal was taken by Mr O’Connor only. His counsel, Michael Lynn, submitted to the three-judge Court of Appeal yesterday that the minister acted outside the scope of their powers in creating an indictable offence.
Conor Power, for the State, said Mr Lynn was attempting to overturn a Supreme Court decision related to milk quotas known as Maher v the Minister for Agriculture (2001).
Mr Power said the habitats directive imposed a positive obligation on the State that a series of measures must be taken to conserve. How else could the directive be effectively transposed into Irish law, he asked.
Reserving judgment, Mr Justice Garrett Sheehan said the court would deliver its decision as soon as possible.
Independent TD Michael Fitzmaurice was present in the Court of Appeal for the hearing.