The 12-week guarantee has been described as "a farce" by Public Audit Committee convener Hugh Henry following hundreds of breaches and an admission that it may not be possible to ensure 100% compliance by Scotland's top health official.
The committee published the findings of its scrutiny of Audit Scotland's study into NHS financial performance and waiting lists.
Health Secretary Alex Neil previously assured the committee that the NHS "are going to get 100%" but said "it may not be possible to ensure that there are no breaches of the guarantee".
The committee's report notes that 100% compliance "will be difficult to achieve".
Mr Henry said: "Our committee has genuine concern that many patients are not receiving the treatment they are fully entitled to receive within 12 weeks of their treatment being agreed.
"During the six months from October 1 2012 to March 31 2013 alone, there were 1217 recorded breaches.
"We have therefore called for the Scottish Government to explain how it will monitor and support the NHS to reduce these breaches."