Audit Scotland carried out the investigation following concerns about manipulation of waiting lists in Lothian Health Board to keep within government targets.
Patients were listed as 'socially unavailable' and the waiting time clock set back to zero, making it appear fewer people were waiting for long periods. The report said there were concerns about how waiting lists were managed and not enough information was available to determine that 'socially unavailable' codes were used properly.
It stated: "The percentage of people waiting for inpatient treatment who were given a social unavailability code rose from 11% in 2008 to just over 30% in 2011."
The auditors mentioned the Western Infirmary and the Southern General in Glasgow as having extensive use of unavailability codes.
Audit Scotland found 900 patients (70%) for orthopedic inpatient treatment at the Western Infirmary were listed as unavailable. For the Southern it was 145 patients equal to 40% waiting for opthalmology listed as unavailable.
It said the unavailability code was introduced in Glasgow in 2011, at a time when there was extra cash to increase capacity and fill consultant vacancies.
An NHS Greater Glasgow and Clyde spokeswoman said: "A number of orthopaedic and ophthalmology patients turned down offers of treatment in one of our hospitals in favour of waiting for a specific clinician or because they wanted to have their procedure in a specific hospital. They were coded as socially unavailable because it was the only code which was not related to a 'medical' reason as to why surgery should not go ahead.
"The reason for them being given this code was to accommodate patient choice without them losing their place on the waiting list."
The opposition claimed the Government was putting targets before treatment."
The Scottish Government said the report showed there was no manipulation in other health boards.