Almost 100 IRA fugitives who were given "letters of comfort" from Tony Blair's government stating they were no longer wanted for past crimes are suspects in nearly 300 murder cases, a senior police commander admitted on Wednesday.

Drew Harris, assistant chief constable of the PSNI, initially told MPs each of the IRA "on the runs" included notorious individuals who were linked to 200 murder investigations – immediately angering unionists already unhappy with the so-called "get-out-of-jail" scheme.

But shortly afterwards, the PSNI was forced to clarify Harris's Westminster testimony by pointing out that these 95 IRA recipients of the letters were of interest in connection with 295 killings from the Troubles between 1969 and 1998.

Northern Ireland's top police officers were giving evidence to the Northern Ireland select committee about the secret scheme Blair's administration hatched with Sinn Féin as part of a wider compact to secure IRA decommissioning of arms and later Sinn Féin's support for policing and the rule of law.

The secret scheme was exposed in the collapse of the prosecution relating to the 1982 Hyde Park bomb atrocity, which killed four soldiers. John Downey was released in February after his legal team produced a letter from 2007, which suggested he would not be prosecuted.

Harris told MPs there were 228 people who had received the letters. He said that some were "notorious, without a doubt" before revealing that "95 of these individuals are linked in some way or other to 200 murder investigations. But that linkage may only be intelligence. And all of that is now being assessed". On hearing that figure, Ian Paisley Jr, the Democratic Unionist party MP, told the committee: "I must say, it breaks my heart today, as a citizen of Northern Ireland, as a citizen of the United Kingdom, 95 people are holding letters excusing the murder of 200 people. That breaks my heart."

Shortly after the hearing ended, the PSNI released a clarification: "A review is currently under way of the 228 names involved in Operation Rapid; 95 of these are linked to 200 incidents involving 295 murders. The link can take a number of forms including intelligence."

Sitting alongside Harris, his chief constable, Matt Baggott, added that only five individuals who had received the letters were now wanted as part of live police investigations for serious crimes including murder. Facing questions from North Down MP Sylvia Hermon, Harris also confirmed there had been only one conviction of an IRA fugitive for a past Troubles crime out of the "on the runs" who had received the letters of assurance.

The chief constable said that a thorough investigation – "Operation Redfield" – was under way into every IRA "on the run" who got the so called "get-out-of-jail" letter. He admitted that on this matter to date the police had "failed".

But Baggott stressed that the PSNI would not give up on investigations into unsolved Troubles-related crimes before 1998, despite the Downey judgment which he described as "unique" to this issue.

He also confirmed that before the establishment in 2007 of a specialist police unit established to deal with unsolved crimes from the conflict – the historical inquiries team – the investigation files into the 228 IRA "on the runs" whom the Blair government had given the letters to had been closed.

The chief constable repeated his apology during the session in front of MPs about the PSNI's mistakes in handling the letter sent to Downey. However, Baggott stressed that the letters were "not amnesties". An inquiry into the on-the-run letters headed by Lady Justice Hallett, which was ordered by David Cameron, is due to report in the summer.

The disclosure was seized upon by hardline unionists opposed to the power sharing government in Stormont. Traditional Unionist Voice leader and European election candidate Jim Allister described the revelation as "yet another shocking part of the callous betrayal of victims which this scheme involved".

The issue of "get-out-of-jail" cards for IRA fugitives wanted for murder has become one of the most controversial issues from the past to haunt the Northern Ireland peace process.

Some victims of IRA violence have begun legal action to test the legal validity of the scheme.

Elizabeth Morrison – a 79-year-old grandmother who lost three members of her family in the IRA bomb on Belfast's loyalist Shankill Road in 1993 just two days after her husband died – has filed papers challenging the controversial deal at Belfast high court.

She has taken the case to try to secure court orders to cancel the on-the-run scheme and discover whether anyone suspected of the Shankill bombing in which nine Protestant civilians were killed has received one of the comfort letters.

The Northern Ireland Office, whose officials originally helped draft the letters of assurance scheme, have refused to disclose to the widow if any of the "on the runs" happen to be suspects in the Shankill bomb massacre.