It was one of the longest and costliest Crown prosecutions in British history, yet the case against Sean Hoey, the only person to be accused of the murders of 29 people at Omagh in August 1998, was emphatically dismissed yesterday by Mr Justice Weir.

The prosecution case was always going to stand or fall on its claim that it could prove that samples of the accused’s DNA could be traced to a series of explosive devices.

The Forensic Science Service (FSS) said that it had found Mr Hoey’s DNA on items relating not just to Omagh but also several other bomb scenes, using a technique it had developed and named Low Copy Number (LCN) DNA. It allows DNA profiles to be uncovered even when there are tiny amounts of DNA present.

The FSS, a government-owned company that is Britain’s largest forensic science provider, began using LCN testing in casework in 1999 and has used it 21,000 times since. It was used to help to convict the killers of Anna Lindh, the Swedish Foreign Minister, and the British backpacker Peter Falconio. But there are doubts among scientists about its merits. The concerns were reinforced by the judge’s examination of expert witnesses.

Putting to one side the technique’s validity, Mr Justice Weir said that the defence was right to have argued that it was up to the prosecution to prove that contamination of the DNA samples had not occurred. He then highlighted instances in which samples could have been contaminated because of poor procedures in their recovery and storage.

But then he went further, singling out “mendacious attempts” by police officers retrospectively to alter evidence “so as to falsely make it appear that appropriate DNA protective precautions had been taken at that scene”. In other words, two officers had lied about how they gathered some of the scientific evidence. They were, he said, guilty of a “deliberate and calculated deception”, adding that he had sent transcripts of the trial to the police ombudsman.

In delivering his verdict, Mr Justice Weir referred to “a most disturbing situation exposed by the defence”. He then spoke of his “concern about the present state of the validation of the science and methodology associated with LCN DNA and, in consequence, its reliability as an evidential tool”.

He said that there was a “need for urgent attention” to quality regulation in forensic science, which the Government said in 2005 it was preparing to answer. The judge said he was “not satisfied either beyond a reasonable doubt or indeed to any acceptable standard” of the “common authorship” of timer power units used in explosive devices that the prosecution claimed could be traced to Mr Hoey.

In conclusion, the judge said the evidence did not meet the “immutable standard” as described in a 1986 appeal case; “evidence so convincing in truth and manifestly reliable that it reaches the standard of proof beyond reasonable doubt”.

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