An officer who shot the first person to be killed by the PSNI was justified in opening fire, Police Ombudsman Nuala O'Loan has said.
But she was critical of aspects of the operation that resulted in Neil McConville's death and that related intelligence went missing afterwards.
The 21-year-old was shot three times as he tried to evade police in a car near Lisburn in April 2003.
Mrs O'Loan said the officer feared the life of a colleague was in danger.
The officer in question was lying in front of the car after being knocked down.
Another man in the car was shot and injured in the incident at Ballinderry Upper. He was later jailed for four years for possesion of a sawn-off shotgun found in the vehicle.
But the ombudsman expressed "grave concerns" that some intelligence information about the police operation had been deleted from a computer during her investigation.
She questioned the police claim that this had been an accident.
Mrs O'Loan was also critical of the police operation on the night of the shooting and said two officers based in the police control room at the time should be moved to other duties.
She also criticised a number of senior officers who refused to co-operate with her inquiries and then retired while possible misconduct issues were being considered.
The police said they had worked hard in recent years to ensure that all officers were aware of their duties and responsibilities to co-operate with police ombudsman investigations.
In a response to the report, the PSNI said: "The police service regrets the death of Neil McConville as we would the death of any citizen who loses their life in the course of a police operation.
"We note the contents of the report and its finding that the officer who fired the fatal shots was justified in using his firearm to protect the life of a colleague.
"Our detailed response to the police ombudsman's other findings is contained in the report itself."
Northern Ireland's police service changed from the RUC to the PSNI in November 2001, as part of sweeping reforms to policing under the terms of the 1998 Good Friday Agreement.