Auditor General Caroline Gardner told MSPs health boards and the SNP administration should have investigated initial signs of issues with the management of patient waiting lists.
Audit Scotland cast doubt on the accuracy of waiting times figures for thousands of patients awaiting treatment north of the Border in a damning report published last week.
It exposed a culture that focused on boards hitting the Government's treatment times targets but not on how the results were being achieved.
The investigation came after the deliberate manipulation of waiting list figures in NHS Lothian. It found some evidence similar tactics may have been employed elsewhere.
Speaking to Holyrood's Public Audit Committee, which is considering whether there has been widespread manipulation of the figures, Ms Gardner said: "We think the focus of attention during 2011 for both the Scottish Government and NHS boards was on whether the 18-week treatment target time was being achieved, rather than how it was being achieved.
"If NHS boards and the Government had been looking at the other information which was available, such as the increasing use of social unavailability codes, that should have raised some warning signs which would have merited further investigation."
NHS managers are being called into the Scottish Parliament to answer questions as the probe continues.
The scandal began in 2011 when it emerged NHS Lothian had been suspending patients from waiting lists to meet treatment times guarantees.
It marked people as being unavailable for operations and appointments for "social reasons" such as being unable to get time off work or being on holiday so they would not appear to be queuing too long.
Audit Scotland's report showed the use of social unavailability codes rising across NHS Scotland from 8% of cases in 2008 to 30% in 2011, and then dropping after the scandal was exposed.
Convener Iain Gray asked Ms Gardner: "Is it your view there was information available to which either the NHS boards or the Scottish Government turned a blind eye, or failed to notice?"
She replied: "It is true that information was available ... on the increase in use of social unavailability codes during that period. That information should have rung warning bells both for the health boards and for the Scottish Government."
She said the information "wasn't acted upon".
Health Secretary Alex Neil has denied any widespread massaging of figures and pointed to new IT systems when asked about the drop in the use of social unavailability codes.
Jackie Baillie, health spokeswoman for Scottish Labour, said: "When asked, Audit Scotland made it clear that, even with IT constraints, there was no reason for health boards to fail to properly document the use of social unavailability.
"The Auditor General again stated the code was used by staff in specialties with the greatest demand. She also emphasised that the IT system, while not perfect, did not explain the dramatic rise and fall in the use of the code."
Ms Baillie added: "Even after the waiting times scandal, the most recent statistics, published this week, can't be relied upon."
Patients are no longer marked as socially unavailable in the same way and explicit agreement is sought from patients if they want a delay to treatment.