Former Chief Constable Sir Ronnie Flanagan says he had no knowledge of the collusion between police under his command and loyalist paramilitaries.
Sir Ronnie Flanagan was chief constable at the time
In a statement issued to the BBC, Sir Ronnie said he hoped anyone involved in such activity would be prosecuted.
NI's police ombudsman found officers colluded with loyalists behind over a dozen murders in north Belfast at a time when Sir Ronnie was in charge.
He is facing calls to quit the body which promotes police efficiency.
In a statement released on Tuesday, Sir Ronnie - currently head of Her Majesty's Inspectorate of Constabulary - said he fully cooperated with the ombudsman's investigation at all times.
"I utterly refute any suggestion, as has been misrepresented in some of the media coverage, that I was in any way evasive or unhelpful," he told the BBC.
SIR RONNIE FLANAGAN'S CAREER
1970: Joined RUC
1992: Promoted to assistant chief constable
1994: Head of Special Branch for six-month period
1996: Became RUC chief constable
1999: Received knighthood
2001: Police Service of Northern Ireland launched
2002: Stepped down from PSNI, joined Inspectorate of Constabulary
2005: Became chief inspector of constabulary
"On the contrary, at no time during the investigation or since did any member of the ombudsman's staff express to me any reservations about my personal action or conduct in any post that I held."
He added: "With respect to the specific matters dealt with in the Ombudsman's report, at no time did I have any knowledge, or evidence, of officers at any level behaving in the ways that have been described.
"I would find such conduct to be abhorrent, and if such behaviour took place my hope would be that it would be the subject of criminal or disciplinary proceedings."
The ombudsman looked into a number of murders
On Monday, Police Ombudsman Nuala O'Loan's report said UVF members in the area committed murders and other serious crimes while working as informers for Special Branch.
Special Branch officers gave the killers immunity, it said.
The report called for a number of murder investigations to be re-opened.
But it is unlikely that any of the police officers involved will be prosecuted - the ombudsman said that evidence was deliberately destroyed to ensure there could not be prosecutions.
Mrs O'Loan said Sir Ronnie was interviewed by her office, but was unable to assist the investigation.
Sir Ronnie led Special Branch before being promoted to chief constable.
On Tuesday, Sinn Fein MP Martin McGuinness said he did not want Sir Ronnie to resign - but wanted him sacked.
Mr McGuinness said: "I have a very strong belief that during the Thatcher era this (collusion) was sanctioned at the very highest level of the British government and Tony Blair knows that.
"I am now calling on him to make a very clear statement about his level of information on what is one of the most damning indictments of British rule in our country in the last 30 years."
SDLP leader Mark Durkan said: "Either he was not in control of a dysfunctional organisation, or he knew full well but kept the truth hidden.
"In either event, he should not head up the Inspectorate of Constabulary."
The body reports on and encourages efficiency and effectiveness of policing in England, Wales and Northern Ireland
Ulster Unionist Policing Board member Fred Cobain said: "If Nuala O'Loan has information about specific officers breaking the law, then that evidence should be given over to the Public Prosecution Service and those officers should be prosecuted.
"What we are concerned about, and I think what the whole community is concerned about, is that this does not end up as a witch hunt."
DUP assembly member Ian Paisley Junior said Mrs O'Loan's report was "very thin on fact but extremely thick on fiction and supposition".
Mark Durkan says Sir Ronnie should resign
"We now have a blanket condemnation and rewriting of the history of the Troubles and of the Royal Irish Constabulary to suit a political objective, and I don't think that serves anybody well in Northern Ireland," he said.
Lord Mayhew, who was Northern Ireland Secretary between 1992 and 1997, said he had no knowledge of any collusion when he was in charge.
He also said he would not pass judgement on Sir Ronnie.
"When a major flaw is found, and that is putting it mildly, in the practice of a police service, naturally enough the buck stops at the top," said Lord Mayhew.
"That said, I am certainly not prepared to make a judgement, cynical or otherwise, concerning what Sir Ronnie Flanagan apparently could remember and not remember."