The judge in the Omagh bomb trial has rejected an application to dismiss some of the charges facing Sean Hoey.
A court artist's drawing of Sean Gerard Hoey
His defence team has claimed there had been "a conspiracy" by a number of police officers to "bury" evidence.
Mr Justice Weir said "the "credibility and reliabilty" of witnesses DS Philip Marshall and forensic officer Fiona Cooper had been brought into question.
However, he said that "any predjudice could be dealt with within the trial process".
The judge declared the conduct of the two police witnesses was "reprehensible".
Mr Hoey denies the 29 murders in Omagh and more Real IRA attacks.
On Wednesday, his lawyer, Orlando Pownall QC, claimed officers had perjured themselves in court.
He said it would not be fair to try Mr Hoey on two charges linked to a mortar find at Altmore Forest, near Dungannon, in April 2001.
The application follows allegations that witness statements had been doctored to give the impression that certain forensic precautions had been taken at the scene, where photographs appeared to indicate that they had not.
Mr Pownall said there had been a "clear indication of a unity of purpose known as a conspiracy" to beef up evidence.
In reply, prosecution lawyer Gordon Kerr acknowledged there had been "impropriety" in the way witness statements had been submitted.
However, he said there was no prejudice to Mr Hoey because the issue had been exposed and explored at trial.
Mr Hoey, 37, of Molly Road, Jonesborough, County Armagh, faces 58 charges in all.
The rest refer to a series of bombings and bomb finds between 1998-2001.
The trial continues.