Former Chief Superintendent Norman Baxter demanded that Mr Justice Weir retract and apologise, claiming the officers had been grievously and publicly wronged, left humiliated, their reputations shattered and personal integrity dissolved.
Innocent people in a modern democracy should not be subjected to such public castigation, he said.
And he added: "I know that if I, as a crown servant in a senior position of authority, had incorrectly and publicly asserted an individual was lying or involved in 'deliberate and calculated deception', I would have been immediately removed from duty by the Chief Constable."
His criticism followed a decision by the Public Prosecution Service in Belfast that the two officers would not be facing perjury charges. Both were investigated by the Northern Ireland Police Ombudsman's Office, who found that part of their evidence which was challenged by Mr Justice Weir was accurate and correct.
The marathon trial ended in December 2007 with the acquittal of Sean Hoey, from South Armagh, who denied murdering the 29 people killed in the Omagh atrocity.
The judge said he believed the officers had not told the truth about the wearing of forensic clothing while investigating an unexploded mortar bomb left at a forest in Altmore, Co Tyrone, in April 2001 - an incident linked to the series of charges Hoey faced.
Mr Justice Weir said he found "deliberate and calculated deception in which others concerned in the investigation and preparation of this case for trial beyond these two witnesses may also have played a part."
His comments were based on a photograph presented to him in court which showed the officers without suits. But the post-trial inquiry confirmed the photograph was taken after they had removed the clothing they wore while examining the scene.
Mr Baxter, 48, who headed the Omagh investigation from May 2002 up until his retirement from a 28-year police career in November last year - said he found the situation incredible.
He said: "I can fully understand why the relatives of those brutally murdered in Omagh on 15th August 1998 lack confidence in the totality of the criminal justice system.
"The wide community in Northern Ireland must be asking 'How can this be? How can a trial which lasted for such a long period of time fail to establish the sequential order of a series of photographs at the Altmore scene?'
"The significant and personal distress and pain caused to my colleagues, who as professional public servants attended court to give evidence in good faith, must also be recognised.
"These police officers found themselves publicly vilified and effectively convicted of perjury by sections of the media. The Police Ombudsman's report demonstrates this was a grave injustice."
The two exonerated officers are Detective Chief Inspector Philip Marshall and Constable Fiona Cooper. Mr Marshall's brother Michael, 25, was shot dead in a IRA ambush on his unmarked patrol car as he investigated a rape allegation in South Armagh in October 1989.
In a statement to the Press Association, Mr Baxter said the officers had been totally vindicated.
He added: "It is difficult to image the injury to human feelings and the public humiliation caused to these public servants over a prolonged period of time. Their reputations were shattered and their professional integrity dissolved. Innocent people in a modern democracy should not be subjected to such public castigation.
"The stain on the character of these officers has now been removed. However, the wording of the judgment remains on the court record and it is my view that Mr Justice Weir should retract paragraph 50 of his judgment in light of the evidence established by the Police Ombudsman.
"Furthermore, police officers directly or through implication accused of lying and 'deliberate and calculated' deception should receive a public acknowledgement that this was not the case, and an apology."
Mr Baxter said there was the wider issue of public accountability of the judiciary in Northern Ireland, and he believed he and his officers had been grievously and publicly wronged by the judge's comments.
He said: "It is correct that judges should raise their concerns about evidence provided by witnesses, but in this case indubitable language was used, while a formal independent investigation was in progress.
"As a consequence intense pressure developed from public representatives and the media demanding that a number of police officers involved in the trial should be suspended and removed from duty. This had a significant and traumatic impact on the private lives of the officers concerned.
"Regrettably, I have to ask the Lord Chief Justice (Sir Brian Kerr), as President of the Courts of Northern Ireland and Head of the Judiciary, to publicly state what his views are on this issue in the context of rulings by the European Court of Human Rights."
