The admission by Drew Harris, the assistant chief constable of the Police Service of Northern Ireland [PSNI], comes three months after the collapse of the Hyde Park bombing case at the Old Bailey in London.
A judge is currently leading a review ordered by the Prime Minister David Cameron into the letters which were issued following a deal struck between Sinn Fein and Tony Blair's Labour Government as part of the 1998 Good Friday Agreement.
Yesterday, Mr Harris told the Commons Northern Ireland Affairs Committee, which is conducting its own investigation into the "on-the-runs" [OTR] letters, that some of the links to the terrorist murders were only obtained through intelligence.
He also said five individuals with letters were under active police investigation on the back of new evidence unearthed by the PSNI's Historical Enquiries Team (HET).
However, Mr Harris told MPs he was not sure if the new evidence related to the five recipients would effectively annul the letters, adding: "that is not clear."
He said files would be passed to prosecutors in Northern Ireland to assess whether charges could be pursued. "I don't know whether they (the letters) will be annulled or not," he said.
Police were asked to review the status of 228 individuals to assess if they were either wanted or not at that the time of the 1988 peace agreement.
Those who were not being actively pursued due to a lack of evidence received a letter from the Government officially informing them of their status.
About 190 republicans were informed they were not being sought by the UK authorities.
The scheme came to light after the collapse of a case against John Downey, 62, who was accused of being the IRA bomber behind at attack in London's Hyde Park on July 20 1982 which killed four members of Royal Household Cavalry, Blues and Royals.
The prosecution of Mr Downey, from Co Donegal, was halted in February after a judge found he had been wrongly sent one of the letters, when in fact the Metropolitan Police were looking for him. Mr Downey denied involvement in the attack.
The judge in the case, Mr Justice Sweeney, said sending the letter to Mr Downey had been a "catastrophic" mistake.
Mr Harris, who was appearing before MPs alongside PSNI Chief Constable Matt Baggott, stressed that evidence linking 95 individuals to terrorist murders may not have been strong enough to justify an arrest.
"That linkage may only be intelligence," he said.
The inquiry into the affair is due to report in the summer.
l A 56-year-old man re-arrested in connection with the 1972 murder of Belfast mother-of-ten Jean McConville has been released pending a police report being sent to prosecutors. The Public Prosecution Service (PPS) will now decide at a later date if there are sufficient grounds to charge him.