The PSNI chief constable has admitted it is now "highly unlikely" that anyone will be jailed for murdering 29 people in the Omagh bombing.
In his first comments since the Belfast Crown Court's freeing of suspect Seán Hoey (38) and the trial judge's indictment of the police handling of the case on Thursday, Sir Hugh Orde defended the second, and current, Omagh investigation as a "genuine attempt to do our very best to re-investigate a crime that had failed to be investigated properly".
He added that former Police Ombudsman Nuala O'Loan's report on the initial investigation had detailed the failures of the RUC's initial response to the 1998 bombing.
Suggesting this had compromised current police efforts to bring a suspect before a court and sustain a conviction, Sir Hugh added: "What we tried to do with the second investigation was to pick up whatever we could from the first investigation . . . and do our best to build a case from those imperfect foundations".
His remarks about the likelihood of a conviction now being secured echo those of former Garda Commissioner Patrick Byrne, who publicly expressed his doubts.
Mr Byrne's comments were attacked in 2000 by former RUC chief constable Sir Ronnie Flanagan, who said at the time: "We will never give up the quest for these people and I am yet optimistic that given further public co-operation we will being these people to justice."
Sir Hugh said that he, like the Director of Public Prosecutions, had hoped the case against Seán Hoey would stand. "The right thing to do was pursue a prosecution albeit with imperfect statements and exhibits," he said.
Sir Hugh said he had "completely reviewed" the manner in which exhibits were handled and stored since the first Omagh investigation. "The evidential chain is now fundamentally different." The chief constable added he accepted full responsibility for the conduct of the second Omagh investigation "under my watch". "I am the serving chief and I'm happy to take responsibility for the current state of affairs."
Under the new policing dispensation, he added, it was vital new witnesses came forward with the type of evidence needed to impress a court. "Realistically speaking, without that, prosecution now is highly unlikely."
Sir Hugh said he would seek "urgent clarification" from trial judge Mr Justice Weir about his fears that the "deception" he referred to in his judgment may have involved more than the two named officers.
"If he can articulate it, I will send it straight to the Police Ombudsman." He said that once the Police Ombudsman reported in relation to the two officers who had given "beefed up" statements to the court he would act on it immediately.
Northern Secretary Shaun Woodward yesterday pointedly failed to give public backing to former chief constable Sir Ronnie Flanagan who is now head of Her Majesty's Inspectors of Constabulary, the British police watchdog.
Also interviewed by the BBC yesterday , Mr Woodward said: "I think it is extremely important that nobody reaches premature conclusions or makes any premature judgements. That obviously includes any implications for the then chief constable, Sir Ronnie Flanagan. So my comments this morning have to be seen in that context."
Efforts by The Irish Times to seek comment from Sir Ronnie's office in London yesterday were unsuccessful.
Policing Board chairman Sir Desmond Rea, in his first comments since the acquittal of Seán Hoey, said the board would meet to consider the judge's verdict. He said the board would meet having read the judgment and then continue to hold the chief constable to account.
Human rights commissions on both sides of the border have called for an independent judicial inquiry into the bombing.
Court cases in England and Wales involving use of Low Copy Number DNA profiling, which was used in the case against Seán Hoey, are now under review.