The Prime Minister has said he does not want to unpick difficult decisions by previous governments to grant Royal pardons to paramilitaries in Northern Ireland.
David Cameron said steps were taken by the last government to get the peace process working.
Royal prerogatives of mercy were issued to shorten the sentences of those convicted of terrorism offences in the period following the 1998 Good Friday peace agreement.
The measure allows changes in prison terms without the backing of, or consultation with, Parliament.
Mr Cameron said: “The last government did have to make very difficult decisions to try to get the peace process started by John Major on track and working.
“I don’t want to unpick all of those difficult decisions, second-guess those difficult decisions.”
Earlier, Northern Ireland Secretary Theresa Villiers told the Commons the Royal prerogative of mercy was used on 16 terrorism-related occasions to shorten sentences, not to cancel offences and not by her government.
Mr Cameron acknowledged that there are still frustrations and issues to be settled in Northern Ireland but added: “We have the basic architecture of devolution and parties working together across historic divides and I don’t want to put that at risk.”
First Minister Peter Robinson has called for the Royal pardons issue to be included in the judge-led inquiry into the on the runs controversy.
DUP MP Nigel Dodds said the Prime Minister should intervene to ensure that the circumstances surrounding the pardons were revealed so people know the facts of the cases.
Dealing with the legacy of the past conflict will form part of renewed five-party talks aimed at resolving outstanding peace process issues.
The negotiations come amid a continuing fallout from the on the runs controversy.
An agreement between Sinn Fein and Labour saw around 200 letters sent to republican fugitives, informing them that UK police were not actively seeking them – but not ruling out future prosecutions if new evidence became available.
The scheme was established following the 1998 Good Friday peace agreement, administered by the Northern Ireland Office (NIO) with the involvement of Tony Blair’s Downing Street and senior law figures.
The process sparked controversy; opponents branded it a grubby deal to win Sinn Fein backing, while supporters insisted it did not constitute an amnesty for murder but was a necessary compromise to support the peace process.
It dealt with cases of republicans suspected of IRA terrorism living outside the UK who were never charged or convicted of related offences.
The special arrangements were disclosed following the collapse of the Hyde Park bomb trial, which was stopped when it emerged the man accused of murdering four soldiers in the 1982 IRA bombing had mistakenly received one of the letters.
John Downey, from Co Donegal, denied the charges.
On Tuesday Northern Ireland’s chief prosecutor said the letters were of no value to perpetrators.
Director of Public Prosecutions (DPP) Barra McGrory QC said the assurances were not an impediment to prosecution if new evidence emerges, and described the government scheme as flawed.
He added that he did not believe any leading members of Sinn Fein had received the messages.
Police are reviewing the cases of those who had received them and a judge, Lady Justice Heather Hallett, had been due to report to the Northern Ireland Office (NIO) on the issue later this month but publication has been slightly delayed, Ms Villiers said.