Police have warned dozens of republicans, including Sinn Fein leader Gerry Adams, their lives are under threat from loyalist paramilitaries.
A document was believed stolen from Castlereagh security complex
It is linked to the discovery of a document believed to have been taken from an Army office in the Castlereagh security complex last year.
More than 20 soldiers were moved to "less sensitive" duties while the probe into the missing document began.
The republicans were told their details were found in paramilitary hands.
Most of those contacted were in the Short Strand area, and included the city's former Sinn Fein deputy mayor, Joe O'Donnell.
On Wednesday, he said that police came to his house and told him the documentation was believed to be in the hands of loyalist paramilitaries.
Some of those on the threat list protested outside a police station
"I'm concerned that once again we have targeting and intelligence gathering by loyalist paramilitaries who just in the last week declared they had no intention of moving the peace process forward," he said.
At the time the file went missing, the then-security minister Ian Pearson said he had been told by senior officers there was no indication it had been given to paramilitaries.
On Wednesday however, Sinn Fein chief negotiator Martin McGuinness accused Mr Pearson and "his senior PSNI sources" of trying to "cover up the clear and irrefutable evidence of collusion between the RIR and loyalist paramilitaries".
"The British government, the British army and the PSNI have consciously allowed over 400 people and their families to live under threat without informing them of this risk for over 16 months in order to sustain the cover-up," he added.
Some of those warned on Tuesday night protested outside a PSNI station in the Short Strand area on Wednesday.
Police said they recovered a document thought "linked to a breach of internal security in Army offices in July 2004".
In a statement on Tuesday, the PSNI said "as a result, police are now warning a number of people about their personal security".
Sinn Fein's Alex Maskey said it was a cause for concern
A spokesperson said on Wednesday they had nothing further to add to the statement.
Police would not say from where exactly the document was recovered or if anyone had been arrested for having it.
Security force sources have indicated that the document was of a type used by the military to assist them in monitoring terrorism suspects.
For its part the Army said it was aware of the police inquiry.
A spokesman said he was not prepared to comment on the outcome of the military's internal investigation or whether action had been taken against any soldiers.