The 56-year-old objected on the grounds of 'double jeopardy', claiming that he should not be subjected to a criminal trial because he has already been punished in prison.
The court was told that Gilligan was found with a mobile phone and a sim card in his cell in Portlaoise and that he had his privileges withdrawn for 56 days.
He was not allowed to exercise with other prisoners, he lost his visiting rights and he was confined to the same cell.
However, today Mr Justice Sean Ryan ruled that the disciplinary proceedings were not a criminal trial and that the issue of double jeopardy did not arise.
He said that double jeopardy could only arise when there has been a previous criminal trial.
The judge refused Gilligan leave to appeal to the Supreme Court and directed that the trial should proceed in the District Court.
