Affidavits sworn by two senior police officers contradict Sir Ronnie Flanagan's response to Ms Nuala O'Loan's criticisms of the Omagh bombing investigation.
They also fly in the face of a affidavit sworn by Mr Raymond White, a former head of both Special and Crime Branch, who claims he never discharged formal investigation responsibility in any criminal investigation, including Omagh.
Mr Alan McQuillan's and Mr Sam Kinkaid's statements, the details of which are known to The Irish Times, state categorically that the controversial investigation was not headed by them when they were the regional police chiefs.
It is understood they reject any blame the inquiry attaches to them.
They claim instead that an effective line of command stretched to Crime Division headed by Mr White, and ultimately to the former chief constable himself.
Mr McQuillan, who became assistant chief constable (ACC) just after the 1998 bombing with responsibility for the North region which includes Omagh, states that Mr White held a leading role in the case.
He asserts that Sir Ronnie appointed Det Chief Supt Eric Anderson as "task force commander" in the case and that his (Mr McQuillan's) role would be limited.
He says further that this view was reinforced by everything he saw of the investigation.
Mr McQuillan also states that Sir Ronnie: did not hold him to account; never asked for information; did not consult him; and did not invite him to meetings with the victims' families.
He says that correspondence and documentation was handled by Mr White and Sir Ronnie, and that Mr Anderson never reported directly to him.
Crucially, he says that weekly Monday meetings of the RUC chief officer team would be briefed on Omagh by Mr White.
The Irish Times further understands that minutes of these meetings support this claim.
Mr McQuillan's affidavit claims he was not consulted on the internal review process which examined the Omagh investigation.
Regarding the police response to the Police Ombudsman, Mr McQuillan states he had no input until January 21st, shortly before it was released.
He says he telephoned Sir Ronnie to express his concern about the paragraph relating to the leadership of the Omagh investigation.
He says he told the officer responsible for drafting the text of the report of what he saw as a critical error twice and understood that a correction would be made.
In his sworn statement, Mr Kinkaid contradicts the affidavit signed by Mr White, saying it is not an accurate description of events and that different arrangements were in place for the Omagh investigation.
Mr Kinkaid also asserts the line of command ran from Mr Anderson, through Mr White to Sir Ronnie and that responsibility did not rest with the regional ACC. He says the inquiry ran on different lines to other serious investigations.
He also claims that paragraph 7.3.1 of the police response to Ms O'Loan's report stated that the regional ACC was not made a member of the investigation management team.
The paragraph he refers to says that the management team comprises a detective chief superintendent as task force controller alongside a senior investigation officer and a deputy.
There is no mention of the local regional ACC holding a position of command.
All three affidavits were drawn up in connection with an appeal by the Police Association to the High Court for a judicial review of the Ombudsman's report.