Detective Chief Inspector William Clark, now retired, said 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 Ardgown Street, Greenock, almost 28 years ago, about whether Ms Doyle's body was covered.
Mr Clark, 77, was the most senior officer there.
He told the High Court in Edinburgh that he took a few steps into the lane, which was only yards from Ms Doyle's home.
Advocate depute John Scullion asked if the teenager's body was covered. "It was, yes, it was covered by a blanket," Mr Clark told the trial. "At that time I had no idea where it came from. I was so angry at seeing it."
Mr Scullion: You told the ladies and gentlemen you were angry?" Mr Clark replied: "Awestruck."
He continued: "As a serving detective officer I knew that should not have happened."
Mr Clark said he asked whether forensic scientists had had an opportunity to examine Ms Doyle and ordered the blanket to be put aside and kept.
"No-one was actually owning up to why the blanket was on the body," he said.
Mr Clark said there were many people milling around. and a police photographer .
"By the time I turned round the blanket had gone from the body."
The body should have been left for forensic examination, he said.
John Docherty, 49, denies murder, has lodged a defence of incrimination and claims he has an alibi.