After health bosses in Lothian were found to have manipulated waiting times targets other board areas were investigated.
The report appeared inconclusive either way, but said lessons need to learned and new systems put in place.
Health Secretary Alex Neil said there was no evidence to back claims of deliberate manipulation.
The section covering NHS Greater Glasgow and Clyde, stated: "Failures in the provision of data or collection of data means they are unable to categorically prove manipulation did not take place."
The row centres on the use of 'social unavailability' where patients are not able to attend hospital for an operation or treatment, and are removed from the waiting list figures.
Mr Neil said: "The reports show that there is no evidence of deliberate manipulation of the figures like those found at NHS Lothian."
But Labour claimed there was no evidence to say there was no manipulation.
Jackie Baillie, Labour's health spokeswoman, said: "There has either been deliberate manipulation of records, bullying, retrospective changes to records or records are so incomplete that no final judgment can be made about what has happened
"Alex Neil has tried to cover for Nicola Sturgeon. His statement was nothing more than a whitewash which failed to recognise systemic failures across Scotland."