Detective Chief Inspector William Clark, now retired, told the murder trial the crime scene had been "contaminated".
The trial, now in its eighth week, has heard differing accounts from officers who were called to a lane off Ardgowan Street, Greenock, in June 1986 about whether 16-year-old Elaine's naked body had been covered to keep her from prying eyes.
Mr Clark, 77, was the most senior officer there.
He told the High Court in Edinburgh he took a few steps into the lane, which was yards from Elaine's home.
He said he was angry when he saw the body covered with a blanket and that no-one owned up to why it was there.
Mr Clark said: "The body had been contaminated to a certain extent by the blanket."
He told advocate depute John Scullion he was "awestruck" at seeing the blanket and added: "As a serving detective officer I knew that should not have happened."
Mr Clark also said an unusual feature of the crime scene was that Elaine's clothes had been piled up neatly beside her.
John Docherty, 49, of Dunoon, denies murder and has lodged a special defence of incrimination as well as claiming he has an alibi,
The trial continues on Tuesday.