NHS boards will be asked to review their waiting time figures within a year to combat concerns that public confidence has been put at risk.
The decision by Health Secretary Alex Neil follows internal investigations, sparked by “fiddled” figures at NHS Lothian, and a wider investigation by Audit Scotland, which scrutinises public spending.
Caroline Gardner, the auditor general, said boards and the Government must improve the monitoring of waiting lists if they are to retain public trust.
Mr Neil, speaking at the Scottish Parliament on the day the auditors’ report was published, agreed with a Conservative suggestion to bring forward the timing of another internal review.
Welcoming the existing reports, Mr Neil said they showed no deliberate misuse of waiting time data.
“No examples were found after extensive investigation of any deliberate manipulation of waiting list records,” he said.
“The Audit Scotland report is entirely consistent with and accords with the findings of the 15 internal audits reported to Parliament by myself on December 20, and where they also found no examples of deliberate manipulation.”
But Labour said Mr Neil used NHS staff as a “human shield” for the Government while accusing ministers of putting spin before patient care.
The waiting lists problem surfaced in 2011 when NHS Lothian was found to have manipulated waiting time codes, marking patients as unavailable for “social reasons” such as failing to get time off work or being on holiday.
Facing extra pressure to meet shorter 18-week guarantees, it was discovered managers were putting pressure on staff to find ways around the system. This included marking patients as unavailable if they refused to travel to England.
Audit Scotland said it had been hard to trace changes on patient records and identify reasons for the use of waiting time codes.
They also found that the use of “social unavailability” increased from 11% in 2008 to just over 30% in 2011.
The levels then dropped off around the time “fiddled” waiting figures were discovered at NHS Lothian.
Auditors found a “small number” of instances when codes were used inappropriately and were often unable to verify reasons.