The top official at the Stormont Department of Justice has said he did not know a Government scheme to deal with fugitive republicans continued after devolution in 2010.
David Cameron has announced a judicial probe following the collapse of a case against a man accused of the 1982 IRA's Hyde Park bomb which killed four soldiers.
The prosecution of John Downey (62), from Co Donegal, was halted earlier this year when it emerged he was wrongly sent a so-called letter of assurance informing him the authorities in the UK were not looking for him.
Mr Downey, who was sought by the Metropolitan Police, denied murdering the troops.
Around 190 letters were sent to on-the-runs (OTRs) under a scheme agreed as part of the peace process, the trial was told.
It sparked fury among unionists, however, who insisted they were unaware.
Nick Perry, senior civil servant at Stormont's Justice Department, said: "I had no knowledge of it continuing after devolution but responsibility for the operation of this scheme and for information being made available about it rests with the (NIO) Secretary of State."
Justice Minister David Ford has said Northern Ireland Secretary Theresa Villiers should have told him about the "shabby backdoor deal".
But he said Mr Perry could not disclose it because of Civil Service rules. In February 2007 the PSNI began Operation Rapid, a review of people wanted in connection with terrorism-related offences up to April 10, 1998, when the Good Friday Agreement was signed.
The review examined what basis, if any, the PSNI had to seek the arrest of individuals identified by Sinn Fein to the Government and passed to the Chief Constable.
It was on the basis of these reviews, the Downey hearing was told, that letters of assurance were sent, or not, to the individual about whose status Sinn Fein had inquired.
This would inform their decisions on whether to travel to the UK.
Mr Perry said he had no knowledge of Operation Rapid.
During private hearings at the Old Bailey before the Downey trial was stopped, it was disclosed that Jonathan Powell, who was Tony Blair's chief of staff, wrote to Mr Perry about the issue in June 2000 when he was in the NIO.
STORY SO FAR
The issue of on-the-runs (OTRs) was thrust into the spotlight through the case of John Downey. Mr Downey was accused of involvement in the 1982 Hyde Park bombing but the case against him collapsed after it emerged he had been sent a letter telling him he was not wanted by police in the UK. The revelation that 190 republican OTRs had received similar letters led to First Minister Peter Robinson threatening to resign. Prime Minister David Cameron ordered an inquiry to be headed by Lady Justice Heather Hallett. Part of the review will be to examine whether other letters have been sent in error, or contained factual inaccuracies.