Trial by jury is set to become the norm in all court cases in Northern Ireland from July next year.
The government is abolishing the old Diplock courts, in which judges heard terrorist cases without a jury.
But the Director of Public Prosecutions can decide that exceptional cases should be tried without a jury if there is a risk of jurors being intimidated.
The SDLP said this exception meant the government's position was "confused", but the DUP insisted it was necessary.
Justice Minister David Hanson said he believed the new system would benefit everyone.
"What we are trying to do is move to a more normal society," he said.
"I want to change the perception that at the moment all terrorist related trials are Diplock-orientated. I want to move back to the jury-orientated.
"But if there are threats perceived, if there are difficulties, the Director of Public Prosecutions can make a request which will be considered by a statutory test to ensure they have a judge-only trial."
SDLP assembly member Alban Maginness criticised the government's position as "confused".
"What we want is the complete abolition of the Diplock court system (which we believe) has been deleterious to the overall perception of the justice system," he said.
However, DUP assembly member Arlene Foster warned that the intimidation of jurors was "still very much a possibility".
"I certainly believe that it is the wrong time to move to trial by jury for every case," she said.
After last year's decision by the IRA to end its campaign, the government promised to repeal its counter terrorist measures, including the no-jury Diplock courts, which date back to the early 1970s.
Twenty years ago more than 300 cases were being tried by Diplock judges during the year - now that figure is down to about 60.
From next summer the Diplock courts will go, but the DPP, Sir Alasdair Fraser, will still have the power to decide exceptional cases should not be put before a jury.
These could involve paramilitaries or former paramilitaries and would be cases where the DPP believed a jury would be open to paramilitary or community-based pressure.
Most cases, however, are expected to be heard by a jury.
To protect juries, the government proposes restricting access to personal information about individual jurors and to restrict the defence's right to challenge members of a jury.
In some cases juries could sit out of sight of the public gallery.
In another change, magistrates will in the future decide if suspects should be freed on bail, not high court judges.
The government is now consulting on its proposals which it intends to put into law during the autumn.