Ruaraidh Nicolson, the assistant chief constable (ACC) for counter-terrorism and organised crime, was found to have carried out a criminal probe into a senior colleague that was not sufficiently thorough or professional.
The Scottish Police Authority (SPA), which oversees the force, cleared Nicolson of misconduct but will raise concerns with Chief Constable Stephen House about "performance-related" matters.
The damaging row, revealed today, involves two senior officers who made their name in the old Strathclyde force.
Nicolson, who was awarded a Queen's Police Medal, rose to temporary deputy chief at Strathclyde before becoming one of the single force's six ACCs.
Detective Superintendent Michael Orr, whose father John was chief constable of Strathclyde police, is the officer who made the complaint against Nicolson.
In January 2010, Kevin "Gerbil" Carroll, a gangland enforcer for the Daniel crime clan, was gunned down in an Asda car park in Glasgow. It was believed the killing was a revenge attack for an attempted hit on a member of a rival gang.
Orr was put in charge of the investigation into the murder, dubbed Operation Trilby.
It later emerged that a corrupt police officer, Derek McLeod, had leaked surveillance information on the Gerbil to a rival gang.
McLeod was jailed for 16 months for breaching the Official Secrets Act and more than two years for drugs offences.
Orr interviewed McLeod as part of Operation Trilby and found himself at the centre of allegations that inducements had been made to McLeod for him to co-operate with Orr's inquiry.
In late 2010, the Crown Office requested a review of Trilby, including Orr's contact with McLeod. The exercise was conducted by Nicolson.
After the review was completed, a criminal inquiry was launched into allegations Orr had attempted to pervert the course of justice. Nicolson conducted this probe. However, the Crown dropped the criminal investigation six months later and no proceedings were ever launched.
A separate misconduct probe led to Orr receiving a verbal warning about a matter not connected to the criminal allegation. Orr, believing the review and criminal investigation had ruined his career, made a formal complaint about Nicolson and another senior officer in 2012.
In his complaint, Orr alleged misconduct in a number of areas. On the review, he alleged Nicolson had failed to engage with him and respond to his correspondence. He also claimed Nicolson did not conduct the review in accordance with established practice.
He further claimed Nicolson had not conducted the criminal investigation in a "thorough and professional manner", adding that he had failed to interview key witnesses and provided inaccurate information to the fiscal.
Finally, he alleged Nicolson had not completed staff appraisals for him between 2005 and 2010.
The SPA, which was still in its infancy, asked the Police Investigations and Review Commissioner (PIRC) to look at the allegations last year. The PIRC drew no conclusions about whether there was a case to answer on misconduct, but offered a summary of its findings.
On the criminal probe into Orr, the PIRC found that Nicolson "did not carry out as thorough and professional a criminal investigation as he should have done".
However, the PIRC said it should be noted that the Crown took no further proceedings against Orr.
On the Trilby review, the PIRC found Nicolson "did not engage with Superintendent Orr during the course of the second review as fully as he might have done".
The watchdog added that this had no marked impact on the outcome of the review.
The PIRC also determined that Nicolson did not carry out appraisals of Orr's performance, adding that Orr and others must share responsibility for this "omission".
The watchdog handed its report to the SPA's Complaints and Conduct Committee in November.
The committee decided the allegations did not amount to misconduct by Nicolson; "however there were a number of performance-related matters which would be drawn to the attention of the Chief Constable".
Nicolson was unveiled as an ACC in December 2012, about four months after Orr lodged his complaint.
The PIRC did not criticise a second senior officer who was also subject of a complaint by Orr.
A PIRC spokeswoman said: "It is the responsibility of the authority to determine what action, if any, it will take on receipt of the report."
Orr declined to comment.
A spokeswoman for the SPA said the body did not comment on individual cases, but added: "The chair of the SPA Complaints and Conduct Committee has held follow-up discussions with Police Scotland about the case concluded in November, including the input from PIRC. This will be formalised in writing in due course."
A Police Scotland spokesman said the force was aware of the PIRC report, but added: "As Police Scotland have not had sight of the contents of this report it would be inappropriate to offer any comment at this stage."