Sinn Féin has insisted that it would have abstained on the renewal of the Offences Against the State Act but it was ultimately not put to a vote after the party's justice spokesperson was outside the Dáil chamber when it was passed.
Matt Carthy had "stepped out" for a few minutes during the debate on the emergency measures that are renewed by the Oireachtas annually.
When he returned, to an almost empty Dáil, he was told by Ceann Comhairle Verona Murphy that the matter had been dealt with.
Earlier, Mr Carthy said that the emergency legislation, which dates back 90 years, should not be used on an ongoing basis.
He called for the the introduction of a modern legal framework to tackle organised crime and to protect jurors.
Minister for Justice Jim O'Callaghan said that he has accepted in principle the recommendations from a independent review group.
It called for the repeal of the act along with the establishment of a non-jury court on a standing basis.
It would be available when ordinary courts were inadequate.
However, he said this would have to be approached with the utmost caution and he indicated that the new system may not be in place before the legislation is due for renewal next year.
The minister said that "dissident republicans", who have their origins in the Provisional IRA and the INLA, continue to pose a threat.
Despite the progress towards peace made over the years, they continue to seek to return to the fruitless violence of the past, he told the Dáil.
"They have remained resolute in their opposition to democracy and rule of law and all that the Good Friday Agreement stands for; and they remain wedded to brutality and criminality," Minister O'Callaghan said.
He said that it is also important not to lose sight of the threat from violent extremism and international terrorism.
The minister added that terrorism - particularly jihadist and lone actor attacks - remains a key risk to the EU’s internal security.
Ireland is not immune from the threats arising in this changed security environment, and the country must have the capability to deal with them, he added.
Referendum may be needed for permanent non-jury court - ICCL
The Irish Council for Civil Liberties (ICCL) said that the Government's plan for a permanent non-jury court may require a referendum.
It said there is a clear clash between human rights and the State's efforts to combat serious crime.
"The Special Criminal Court is a non-jury court and the right to a jury trial, we feel, is an absolutely fundamental right in a democracy," ICCL Executive Director Joe O'Brien told RTÉ's Drivetime.
"If that's going to be taken away, it has to be looked at very seriously and there has to be checks and balances."
Mr O'Brien said the arguments that are being put forward "year-on-year" for the Oireachtas to give the court "statutory provision and legal position to operate" are becoming "weaker and weaker".
"It was established at a time during the Troubles under emergency legislation ... and what we have seen the Special Criminal Court used for increasingly over the years is gangland violence and gangland crime as well ... something that other jurisdictions have, other common law jurisdictions, in England and USA and Australia, face on a regular basis and they do so with jury courts," he said.
