The Northern Ireland Affairs Select Committee, sitting at Stormont, is hearing submissions from those involved and those potentially affected by the OTRs scheme.
Around 200 letters were sent to republicans under an agreement between Sinn Féin and the last Labour government, informing recipients that UK police were not actively seeking them.
The letters did not rule out future prosecutions if new evidence became available.
"I would argue as a prosecutor that they are of no value," Mr McGrory said on Tuesday.
"Anyone who is in receipt of these letters ought not to be sleeping easy in their beds."
It is my professional opinion, as the chief prosecutor of the jurisdiction, that these letters are of little benefit.
Barra McGrory QC
Mr McGrory said that if evidence was to be found by police regarding any of the OTRs, "if it meets the evidential test, then the individual will be prosecuted".
Prior to his appointment as DPP, Mr McGrory had some involvement in the administrative scheme as a lawyer representing Sinn Féin, but he had said that he was never involved in the strategy behind it.
The letters came to light when the trial of Donegal man John Downey, who had been charged with murdering four soldiers in the 1982 IRA bombing of Hyde Park in London, collapsed.
It emerged that the accused, who denied the charges, had received one of the letters.
DUP First Minister Peter Robinson also appeared before the committee on Tuesday.
"I have to say that I was appalled that such a scheme was ever put in place and equally concerned that it was being done in a covert way," he said.
"The scheme was hatched in the full knowledge that victims could be denied the possibility of justice. It was inequitable, sectarian - a concession to republicans alone.
"It was deceitful and carried out behind the backs of two sets of unionist negotiators and involved consciously supplying false assurances and disingenuous answers to direct queries."
The fact that one of these letters was used to allow someone who was a terrorist suspect to avoid trial represents a deeply damaging blow to the concept of justice.
First Minister Peter Robinson
Sinn Féin has been criticised for not sending Gerry Kelly, who was involved in the administrative scheme, to give evidence to the committee.
However, Mr Kelly has defended that decision on the grounds that he and his party considered the process a "sap to unionism".
According to figures released to UTV by the PSNI under Freedom of Information legislation, police reviewed 228 names for the Northern Ireland Office between 7 February 2007 and 9 September 2013 as part of Operation Rapid.
Of those names, 95 were linked to 200 incidents involving 295 murders.
Attorney General John Larkin QC attended the committee hearing on Tuesday and discussed the issue of whether suspects could have been tipped off if they had applied but were refused a letter.
He claimed that could have amounted to being told to "stay where you are" in order to avoid arrest.
"It strikes me that the aspect of the scheme which has been relatively under-explored has been the indication, by whatever means, to individuals that the police are still looking for them," he said.
Mr Larkin said he hoped care had been taken to avoid tipping someone off or perverting the course of justice before any indication as to their 'wanted' status could be given.
But he added: "If it wasn't, if there was a carelessness or worse, then indeed one would expect that to be properly looked at."