Sinn Féin has described the arrest of six people, including one alleged to be the IRA's director of intelligence, as extremely provocative.
The party said Saturday's arrests, which were made in connection with a raid on Castlereagh police station, were part of a cover up while senior unionists said they raised serious questions about the peace process.
Hundreds of police officers and British soldiers conducted a series of high-profile operations in Belfast and Derry early on Saturday morning.
Four men and two women were arrested, two men and one woman were released without charge yesterday.
The others were still being questioned last night.
The affair began when three men gained entrance to a Special Branch office in the Castlereagh PSNI station in east Belfast on St Patrick's Day, overpowered a detective and stole a number of documents.
It is believed the documents contained information including addresses and phone numbers of both special branch officers and their informants in Belfast.
Up until the arrests were made most indications, including those from the Chief Constable Sir Ronnie Flanagan had been that the raid was conducted by a group within the security services with much suspicion directed at British military intelligence.
On Saturday, however, police sources said they now believed those responsible were linked to the Provisional IRA.
One of those arrested had been working as a civilian in the complex, they said.
Security sources said another of the arrested men was believed to be a senior figure in the IRA.
Sinn Féin said it had raised the matter with both the Taoiseach's office and Downing Street.
Its chief whip, Mr Alex Maskey, said suggestions of republican involvement were "ridiculous and insulting to people's intelligence".
"The security forces' actions are extremely provocative to republicans when you consider that this Easter weekend people all over Ireland will be commemorating their history, culture and heritage and when you consider that republicans have been trying to consolidate the peace process," he said.
"It would seem to suggest that there is panic going on within the security services about this break-in and I fear that we could be entering a dangerous period," he said.
Mr David Burnside, the Ulster Unionist MP for south Antrim said there would be huge implications for the peace process if it were established that the IRA was behind the Castlereagh break-in.
"If it is Sinn Féin-IRA who were behind this incident, then it would make sense as they have been trying to use black propaganda to undermine the Special Branch," he said.
"Setting aside the security implications, I would argue this also has huge implications for the political process.
"If this is the IRA, the Provisional IRA who are inside the process and in the government of Northern Ireland, unionists and my party colleagues are going to have to re-examine their whole approach.
"You can't have Martin McGuinness's colleagues playing a game by day of being in politics and then a game by night of engaging in illegal terrorist activity," he said.