The Minister's action relates to Bernard otherwise known as Brian Kilgariff, who as a senior official with the Department of Agriculture had investigated animal welfare issues.
In June Mr Kilgariff was convicted before Sligo District Court of animal neglect and animal welfare breaches, along with failing to have his animals tested for TB and Bovine Viral Diarrhoea (BVD) since 2016.
The allegations on the summons before the District Court included that he had breached the 2015 Disposal of Carcases Regulations.
Mr Kilgariff pleaded guilty to two charges relating to the testing breaches, and to four of 10 charges relating to neglect, or being reckless regarding the health or welfare of an animal.
Judge John Kilraine gave Mr Kilgariff (64) of Bricklieve, Castlebaldwin, Co Sligo a four-month suspended prison sentence on each of the charges relating to the animal carcasses.
Mr Kilgariff was also convicted on the two testing charges and fined €1,000 in each matter.
In High Court judicial review proceedings, the Minister claims that the District Court judge erred in law and acted in excess of its jurisdiction by imposing a concurrent four month suspended prison sentence in respect of offences concerning the disposal of animal carcasses.
The maximum penalty that could be imposed for such an offence committed under the regulations is a fine, the Minister's lawyers submitted.
As a result, the Minister says that the suspended sentence and the conviction should be quashed. The Minister does not want the matter remitted back before the District Court.
The Minister also claims that the remainder of the District Court's order against Mr Kilgariff, is valid and should remain intact.
This includes an order under the 2013 Animal Welfare Act disqualifying him from holding a herd number for five years, which the Minister says was lawfully made and within jurisdiction.
The Minister's application came before Ms Justice Nuala Butler at the High Court on Thursday.
The judge said that she was satisfied, on an ex-parte basis, to grant the Minister permission to the bring the challenge in which Mr Kilgariff is the respondent to the proceedings.
The judge also placed a stay on the conviction and the suspended sentence imposed on Mr Kilgariff.
The action will return before the Court in October when the new legal term commences.