The Police Ombudsman for Northern Ireland has said it did not make a complaint to police that led to the arrest of two journalists.
But Durham Constabulary has maintained that the ombudsman's office did report the theft to police.
Barry McCaffrey and Trevor Birney were arrested over the suspected theft of documents from the ombudsman.
The confidential documents related to a police investigation into the murder of six men in Loughinisland.
Mr McCaffrey and Mr Birney produced a documentary about the 1994 killings.
It was reported at the time that the ombudsman reported the suspected theft to the police.
BBC News NI understands that staff from the ombudsman's office raised concerns with the PSNI that a document shown in the documentary may result in a security risk for individuals named in it, but did not report that the document was stolen.
The statement said: "The day after we had a viewing of the documentary, we briefed the Police Service of Northern Ireland that it had identified a number of individuals who may now be at risk.
"It had shown extracts from what appeared to be a Police Ombudsman document, albeit in a different format to our document".
"We did not make a complaint of theft.
"We understand that the PSNI commissioned Durham Police to investigate the means by which the film's production team secured access to the material, whether by theft or disclosure".
The PSNI told BBC News NI they were unable to comment due to ongoing legal proceedings.
'Definite and clear'
However, in a subsequent statement to BBC News NI, Durham Constabulary Chief Constable Mike Barton said: "The Office of the Police Ombudsman for Northern Ireland (OPONI) did report the theft of their material to the PSNI at a meeting on 4 October 2017 immediately after identifying the fact that 'secret' documents, created by OPONI, had featured in a documentary film.
"This criminal investigation has a definite and clear starting point.
"The report by OPONI was subsequently followed up by a written statement of complaint by a member of their senior management team.
"The statement acknowledges that, following this initial report, Durham Constabulary would be conducting a criminal investigation into theft or other unauthorised disclosures."
The inquiry centres on the suspected theft of sensitive material, which was used in the No Stone Unturned documentary, which examines claims of state collusion in the murders.
Detectives from Durham Constabulary, supported by PSNI officers, searched two homes and a business premises in Belfast in August.
They seized documents and computer equipment during the searches.
But the material will not be examined by police until the outcome of a legal challenge by the company that produced the film.