A police agent penetrated the IRA's central structure and played a key role in the Police Service of Northern Ireland's offensive against IRA intelligence gathering, according to a security source.
The PSNI claimed on Monday it had smashed an IRA espionage operation at the heart of Stormont and at the former RUC Special Branch offices in Castlereagh.
Sinn Féin's chief negotiator, Mr Martin McGuinness, said yesterday that nobody should be involved in spying.
According to a "senior security source" quoted by BBC Radio Ulster yesterday, the crackdown on alleged IRA intelligence gathering was aided by a police agent operating "deep within the IRA".
Since the alleged security breach at Castle Buildings in Stormont was publicly disclosed in early October, four people have been arrested and charged. The PSNI Special Branch, co-operating with MI5, also hoped to charge the IRA's director of intelligence from west Belfast in connection with the alleged IRA spy ring, the BBC reported.
While the reputed IRA intelligence chief was questioned at the time, he was not charged. The BBC also reported that the security agencies have been carrying out surveillance and bugging of the IRA's intelligence network for a considerable time.
The then Northern Secretary, Dr John Reid, was aware of the IRA's penetration of the NIO in July, when in the House of Commons he warned the IRA to end its paramilitary activities.
On Monday, the new acting deputy chief constable, Mr Alan McQuillan, said that a small number of IRA agents had been operating at Stormont.
As a result of the security investigation, code-named Operation Hezz, which follows last St Patrick's night break-in at the Special Branch offices at Castlereagh station and the Stormont infiltration, the PSNI had destroyed "a major intelligence unit within the IRA", Mr McQuillan said.
The investigation took police "into the heart of the IRA", he added. As part of the investigation, which involved a team of 40 detectives, police seized a huge quantity of documentation, some of which was allegedly stolen from the NIO and some of which was allegedly IRA material.
Judges, forensic scientists, police officers, British military personnel and loyalists were warned about their personal security because details about them had fallen into the hands of the IRA, according to Mr McQuillan.
The acting deputy chief constable said he could not say whether any of the information unearthed in the investigation had been handed on from the IRA to Sinn Féin.
Mr McQuillan said that while the IRA was involved in intelligence gathering, he did not believe it planned to use its information in any "offensive way". The investigation was continuing and he hoped there would be further arrests, he added.
The former Sinn Féin education minister, Mr Martin McGuinness, said he believed the operation was part of an "anti-peace process agenda" being pursued by a "substantial section of the PSNI".
"Let me say very clearly," he added, "if there are people out there involved in spying then they shouldn't be, it's wrong and they should stop."
"One of the revealing things that McQuillan said was his belief that the IRA cessation was not under any threat whatsoever. Let's work on the basis that the IRA are committed to the success of the peace process," he added.
Mr McGuinness said Mr McQuillan's hope of making further arrests reinforced the belief that "a witch-hunt" against Catholic civil servants was under way.
Former Ulster Unionist minister Mr Michael McGimpsey called for a public inquiry into the allegations against the IRA.
SDLP leader Mr Mark Durkan said the IRA needed to be completely dismantled to end the allegations. "Those who have helped the peace process in the past with ceasefires... need to bring forward a cease-army situation," he added.
