The assurance letters sent to around 200 Irish republicans assuring them they were not wanted by police did not amount to a terrorist amnesty, a review has found.
The scheme, which resulted in the collapse of the trial of John Downey, who was accused over the 1982 Hyde Park bombing, was "flawed" and "unprecedented", the inquiry found, but was not "unlawful".
However, the letter sent to Mr Downey assuring him he would not be prosecuted was a mistake caused by a system "open to error" and the review found that two further letters had been wrongly sent.
One letter was sent out to a potential offender after police used the wrong date of birth to search a database, which would have shown up a linked offence.
The second letter was sent out although the suspect was wanted for an offence committed after the Good Friday Agreement.
Lady Justice Hallett, who led in the inquiry, said: "The administrative scheme did not amount to an amnesty. Suspected terrorists were not handed a 'get out of jail free card'."
Announcing the conclusions of the review in the House of Commons, Northern Ireland Secretary Theresa Villiers said: "So I repeat again today to the people holding these letters, they will not protect you from arrest or prosecution and should the police succeed gathering sufficient evidence, you will be subject to due process of law."
The judge-led review into the so-called "amnesty letters" scheme, which started in 2000, was ordered after the collapse of the trial of Mr Downey in February after a judge ruled the letter meant he could not be prosecuted.
The Police Service of Northern Ireland (PSNI) sent the letter even though Mr Downey was wanted by the Metropolitan police - when they realised the mistake they did not act.
Lady Hallett said the PSNI's failure to do anything about the error was "inexplicable in law and logic".
However, she found that the collapse of the trial against Mr Downey did not set a precedent in law and it did not mean that others with letters could not expect to find themselves before the courts.
The case triggered a crisis in Northern Ireland leading the Democratic Unionist First Minister Peter Robinson to threaten to resign.
He welcomed the report saying it confirmed the scheme was "wrong in principle" and "shambolic in practice".
Mr Robinson had claimed he knew nothing about the letters, however, the review found that the deal between Tony Blair’s Government and Sinn Fein in the wake of the 1998 Good Friday Agreement was not a "secret".
It found Mr Blair gave Sinn Fein President Gerry Adams an assurance steps would be taken to resolve the issue of on the runs, which was seen as an issue of genuine importance to the peace process.
Under the terms of the Good Friday Agreement the early release of those convicted of terrorist offences during the Troubles was agreed, however, it left the question of what to do with those wanted for crimes.
The inquiry found 228 names were put forward for consideration for the scheme by Sinn Fein, the Irish Government, and the Northern Ireland Prison Service.
Of those, 156 were given letters of assurance that they were not wanted, 31 were told they were not wanted some other way, 23 were told they were wanted and 18 have not been made aware of their status.