NHS chiefs did not brief the Health Secretary about changes in the number of patients being marked as unavailable for treatment until after problems emerged at NHS Lothian, MSPs were told.
Derek Feeley, the chief executive of the NHS, condemned deliberate manipulation of waiting times, as happened in the Lothian health board area, as "unacceptable".
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, including marking patients as unavailable if they refused to travel to England for treatment.
Mr Feeley said that while there was a "big peak" in the number of patients across Scotland classed as being socially unavailable for treatment in December 2010, this was not flagged up to then Health Secretary Nicola Sturgeon.
The NHS chief executive told MSPs on Holyrood's Public Audit Committee: "We did have a discussion with the Cabinet Secretary about the winter pressures, but we didn't have a specific conversation about social unavailability."
Mr Feeley and other senior figures from the NHS appeared before the committee less than a month after ministers were warned that trust in official targets has been put at risk.
Committee convener Iain Gray demanded to know if anybody in the NHS had "felt it was worth drawing the Cabinet Secretary's attention to the fact there was a tripling in the use of social unavailability codes".
But John Connaghan, director for health workforce and performance in the Scottish Government, told him: "There was no cause for concern during that time period."
In its report, Audit Scotland said their work had been hampered by a lack of information and because of inadequately-controlled management systems. Mr Feeley said the Government accepted Audit Scotland's recommendations and would act on them.