In his verdict, clearing Sean Hoey of all charges, Mr Justice Weir referred to "a most disturbing situation exposed by the defence".
Laganside Court, Belfast
He felt such disquiet about evidence given by two police witnesses over forensics that he had sent transcripts to the police ombudsman, he said.
The judge said he found "deliberate and calculated deception".
This "made it impossible for me to accept any evidence given by either witness," he said.
"Since I have no means of knowing whether they may have told lies about other aspects of the case that were not capable of being exposed as such."
He described the arrangement by police in 1998/99 for storing forensic items as "thoroughly disorganised".
Labels were missing from items or incorrectly attached to the wrong item, the judge said. There were examples of labels lying loose and bags without labels.
"There was no universal system of logging items received, no proper recording in police stations so no inventory of what was in a store at any particular time," Mr Justice Weir.
"For a major incident there should be a specific exhibit book but these were not always opened or properly maintained."
He said one scenes of crime officer had described the police's special property store in Newry as "a complete mess".
There was therefore no system for verifying what had been collected or what was then placed in the police store, Mr Justice Weir told the court.