Scotland's public sector watchdog said it was unable to say whether NHS waiting list manipulation had taken place, due to "poor" information.
In a small number of cases, it said patients were inappropriately marked as unavailable for treatment, but could not say whether these were deliberate.
Audit Scotland said the management and scrutiny of the system "had not been good enough".
Health Secretary Alex Neil insisted the problem was "historical".
Speaking on BBC Radio Scotland's Good Morning Scotland programme, the minister admitted that IT systems had not been robust enough but that was now changing.
He added that the ability to list patients as "socially unavailable", thereby removing them from the waiting time system, no longer existed.
Audit Scotland investigated after problems came to light in NHS Lothian and in Tayside.
They were criticised for removing patients from the 18-week waiting list when they refused to travel to England for treatment, marking them as "unavailable for social reasons".
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It also emerged that some staff at NHS Tayside said they felt under pressure to say patients were "unavailable" for appointments in order to meet waiting-times targets.
The latest Audit Scotland report - which covered the period when Lothian waiting lists were being manipulated, between April and December 2011 - said there was "widespread use across Scotland" of the social unavailability patient code during that time.
It said use of the code rose from 11% of patients in 2008 to more than 30% in mid-2011, which came during a time when waiting time targets were being shortened.
Audit Scotland also said key areas of waiting time systems were inadequate.
It said limited information in the records of patients waiting for treatment meant it was not always possible to identify changes or check that status codes were applied appropriately.
'Better scrutiny'The figure started dropping at the end of that year, but Audit Scotland said the reason for this was unclear due to the lack of available information.
"Audit Scotland found a small number of instances where unavailability codes were used inappropriately," the watchdog stated.
"Due to the poor information, it was not possible to determine whether these were due to human error, inconsistent interpretation of guidance, or deliberate manipulation."
Scotland's auditor general, Caroline Gardner, said: "The management and scrutiny of the waiting-list systems have not been good enough.
"During the period we reviewed, the Scottish government and boards were focussed on making sure waiting times targets were being met but not giving enough attention to how this was being done.
"Better scrutiny of the increasing use of social unavailability codes could have highlighted concerns earlier. It also could have identified where waiting times pressures were building in the system."
NHS Greater Glasgow and Clyde: In the electronic system used in the south of Glasgow, the full patient record was not accessible once a patient was removed from the waiting list.
NHS Grampian: Records often had no information recorded about why social unavailability was applied.
NHS Forth Valley: Good practice in the way information was recorded in its electronic waiting list system, with detailed notes in patient records.
Covers period from April-December, 2011
Mr Neil said most of the recommendations in the Audit Scotland report were already being implemented.
He told the BBC: "Patients are happy with the waiting times, what we are unhappy with is - now an historical situation - is the lack of robustness in some of the IT systems to record the detail of information that we need."
Mr Neil said the social unavailability code was replaced in October by a new system giving patients more flexibility to agree when they want to be treated.
The explicit agreement of patients is also needed if they want their treatment to be delayed.
The minister has announced that a pilot phone line for patients seeking advice on waiting times will be opened later this year.
The health secretary said work was also under way to make sure patients knew their rights.
Labour health spokeswoman Jackie Baillie said: "This report makes clear that hidden waiting lists were widespread, not just in Lothian, and the SNP government was aware there was a problem and did nothing.
'Bizarre rise'
"It preferred to believe it's own spin and hype than concern itself with what was really going on in our hospitals."
Scottish Conservative deputy leader Jackson Carlaw added: "If you look at the trends presented here, it is difficult to reach any other conclusion than the deception used by NHS Lothian may well have been mirrored elsewhere.
"If that isn't the case, the Scottish government needs to explain why there was such a bizarre rise in patients who became unavailable over a fairly short period of time."
Liberal Democrat MSP Jim Hume said: "This report takes the gloss off of the SNP government's record on waiting times targets.
"People across Scotland will find the report's findings disappointing and unsettling given that, prior to the waiting-times scandal coming to light, as many as 30% of inpatients in Scotland were marked as socially unavailable."
Iain Gray, convener of Holyrood's cross-party audit committee, said it would be looking into the issues raised in the report, adding: "Patient wait times are a major NHS performance target and extremely important to the patients themselves."
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