The Minister for Justice, Mr O'Donoghue, has said the granting of immunity to supergrasses was in the common good where it ensured the conviction of those involved in heinous crime.
Speaking on RTE's Prime Time last night, Mr O'Donoghue said it was "entirely wrong" to suggest there was a comparison between the Diplock Courts in the North and accomplice evidence given in the Special Criminal Court.
Recent years had seen a growth in organised crime, money laundering and drug trafficking in Ireland and society was entitled to put in place a mechanism to fight this, he said. The witness protection scheme was such a mechanism and was legitimate where the threat to society was grave.
The courts must make it clear that where there was evidence given by accomplices there was a doubt over it and that it should be corroborated by other evidence, said Mr O'Donoghue.
The jury, having been alerted to the dangers, would then go on to consider the corroborative evidence and would have to be satisfied beyond a reasonable doubt.
He stressed that where the Director of Public Prosecutions brought such cases to the Special Criminal Court he must have been of the opinion that it was "the right thing to do".
Safeguards had been built into the witness protection system to take into account the nature of accomplice evidence.
"There are exceptions where the granting of immunity is in the interests of the common good when it ensures the convictions of people involved in heinous crime," said Mr O'Donoghue. The system was not there to threaten innocent citizens but those who were involved in organised crime, laundering money and drug trafficking, he said.