Donald Findlay QC said that detectives did not properly secure the area in Greenock, Inverclyde, where 16-year-old Ms Doyle's body was discovered in June 1986.
At the High Court in Edinburgh yesterday, Mr Findlay said the way officers acted had caused evidence that was collected at the scene to become contaminated.
Mr Findlay said that DNA evidence against his client John Docherty, 49, was unreliable.
He said that the jury could not trust it when it came to consider its verdict.
Comparing the police investigation to a poisoned tree, Mr Findlay told the jury: "When a tree is poisoned it isn't just the tree that is poisoned; the fruit of the tree is poisoned and you should never eat the fruit of the poisoned tree."
Mr Findlay also suggested that some police officers who had given evidence at the trial had told lies about what happened in the early stages of the investigation.
Mr Findlay was speaking to the jury on the 50th day of proceedings against Mr Docherty, of Dunoon, Argyll who denies murdering Ms Doyle on June 2 1986.
The advocate spent the entire court day delivering his closing speech without referring to notes.
During his address, Mr Findlay said that when police were collecting forensic evidence from Ms Doyle's body, officers did not wear protective clothing.
The trial in Edinburgh, which is being heard before Judge Lord Stewart, will continue on Monday.