Health Secretary Alex Neil said the waiting times audit reports showed "no evidence of dishonest or wide scale manipulation of waiting times across the NHS in Scotland" during a ministerial statement on 20 December 2012.
All 14 Scottish health boards had been asked to review their practices in light of the manipulation of waiting time figures in NHS Lothian and then accusations of the same at NHS Tayside.
Mr Neil said: "This is the largest investigation into the management practices of waiting times ever carried out in NHS Scotland."
"Overall the waiting times published by boards are reliable and accurate".
The health secretary said all health boards would now put in place improvements in the way in which information is captured and the way it is reported.
The audit of NHS Tayside found some staff felt they were bullied into fiddling waiting times figures.
It found that in 17% of the cases that were checked, patients had been systematically deemed to be unavailable for treatment so that they didn't breach the waiting time guarantee.
The board has apologised to patients and says its put controls in place to ensure these practices have been eradicated.
Two members of staff who were suspended have now returned to work.
Scottish Labour health spokesperson Jackie Baillie said it was beyond any doubt that the "awaiting times scandal had deepened", highlighting NHS Lothian and Tayside and claiming the Scottish government were guilty of a "whitewash".
She said: "instead of leading the NHS they are misleading Scotland and the thousands of patients affected by this scandal."
The health secretary hit back saying her "scaremongering was totally unfounded and her allegations were totally without foundations" adding her attack, "effectively on the NHS staff was totally outrageous".