As part of the Treatment Time Guarantee, which came into law in October 2012 and is intended to offer a guarantee of treatment for many in-patient procedures within 12 weeks, health services are supposed to write to patients to inform them of their rights.
They must also tell patients of any changes to how long they can expect to wait if people tell the NHS they are temporarily unavailable for treatment.
However, a series of internal audit reports on management of waiting lists - ordered by the Scottish Government after it emerged in 2012 that NHS Lothian had fiddled statistics by changing records to classify patients as unavailable for treatment - has revealed more than a quarter of the country's 14 health boards have not been following the rules.
In the NHS Highland probe it was found that while the board should have written to patients during seven possible scenarios, including informing them of their legal right if they were removed from a waiting list or if their right was to be breached, systems were not in place to do so, leading to a risk the board was not complying with the law. It was planned that software to rectify the issue would be in operation by this month.
In NHS Shetland, investigators found none of a sample of five patients had received a letter to say they had been put on a waiting list or that a period of unavailability was applied, while one was not sent a letter to confirm they were offered an appointment date.
In NHS Lanarkshire, which serves a population of more than 500,000, auditors said there was a risk letters may not be produced or retained as an IT system was still being upgraded, potentially leaving the board open to litigation.
In NHS Western Isles, no patients selected in a sample received letters advising them of unavailability and how it affected their waiting time. Investigators were later told by management that a software issue meant automatic issuing of letters "did not work", although it is understood the issue has now been resolved.
The Government said it had sought reassurances from boards that patients were being informed of their rights, following the internal investigations, which were completed in October and November and have been made public under Freedom Of Information laws.
However, Hugh Henry, Labour MSP for Renfrewshire South and convenor of the Scottish Parliament's Public Audit Committee, said the findings raised further questions surrounding the Treatment Time Guarantee legislation.
He said: "The Cabinet Secretary had indicated to us (Public Audit Committee members) that where boards were not complying patients would be written to. This seems to contradict that. All of these things should have been thought through before the proposal was made to implement the Treatment Time Guarantee and Parliament was asked to approve it."
The Guarantee has come under increasing scrutiny in recent months with thousands of patients, largely in the Lothian and Grampian areas, set to have their legal right breached this year.
The Government has demanded recovery plans are put in place, with NHS Grampian saying it will be compliant with the law by the summer and NHS Lothian planning on meeting it in all cases by next January.
A Government spokeswoman said: "We have sought reassurances from boards that all patients are being informed of their rights under the Guarantee.
"In the small number of case where letters cannot be issued, due to upgrading required on local IT systems, patients are receiving calls from health professionals to advise them of their rights."