The finding appeared in an NHS Tayside report sparked by allegations of fiddled waiting times figures.
All 14 Scottish health boards had been asked to review their practices in light of the NHS Lothian accusations.
NHS Tayside has apologised, adding it had now put controls in place to ensure such practices had been eradicated.
It had also allowed two members of staff who had been suspended to return to work.
In a statement to parliament, Health Secretary Alex Neil said the reports showed no evidence of deliberate manipulation of the figures, but there were improvements in waiting times management that could be put in place.
He told the chamber that the ability to list a patient as "socially unavailable" no longer existed.
Continue reading the main storyOther health boards have retrospectively adjusted their figures, social unavailability is at an all-time high of almost 21,000 at June 2011, now dropped to 9,500 as of September 2012 - that is nothing short of a miracle”End Quote Jackie Baillie Labour's health spokeswoman Mr Neil said it would be replaced by a new system where patients would decide themselves when they wanted to be treated.
He added: "Staff need a system which is easy to work with, where the rules are clearly understood and which are transparent to patients and their carers.
"Improvements in IT are already taking place and I have been clear this work should be finished by April 2013.
"An investigation of this scale into the management practices of waiting times has never been done before, with over 2.5 million transactions over a six-month period reviewed to identify any trends which needed further investigation."
The focus on waiting times logging came about when NHS Lothian was criticised in October for removing patients from the 18-week waiting list when they refused to travel to England for treatment.
Some patients were referred to Northumberland but, when they declined to go, they were marked as "unavailable for social reasons" and not included on the waiting list.
In a heated chamber exchange, Labour's health spokeswoman, Jackie Baillie, told Mr Neil the reports' contents demonstrated "beyond any doubt" that the "SNP waiting times scandal has just deepened".
She said Mr Neil's statement "was a whitewash and full of assertions".
Ms Baillie added: "Nicola Sturgeon assured this chamber that she had spoken to all health boards and this was only a problem in Lothian."Then came NHS Tayside - evidence revealed today of blatant waiting times manipulation, serious allegations of bullying and pressure being applied to staff.
"And the problem is wider - other health boards have retrospectively adjusted their figures, social unavailability is at an all-time high of almost 21,000 at June 2011, now dropped to 9,500 as of September 2012 - that is nothing short of a miracle.
"The one thing is clear, the manipulation for waiting times is rife."
However, the Tories Jackson Carlaw welcomed Mr Neil's statement and said he was relieved to see that widespread systematic failures were not evident.
He told the chamber: "This scandal began because we accepted at the time the cabinet secretary Nicola Sturgeon was serially misled by Lothian health board at the time - the allegation thereafter that there was a widespread systemic collapse across Scotland was the reason this investigation was undertaken.
"I think patients across Scotland will actually be relieved to find that the suggestion that is the case is not borne out by the detail in the investigation that has taken place."
However, he added that the recommendations now being made should have been in place without having to be asked for.
Staff misunderstandingAfter publishing its report, NHS Tayside said it was disappointed that "unacceptable practices" had been identified in a "small area" of waiting times management.
A spokesman said: "We very much regret that this has happened, apologise to patients and reassure them that we have put controls in place to ensure these practices have been eradicated.
"Patients are our priority and, therefore, as soon as we were alerted to a potential issue by our internal auditors, we immediately carried out an in-depth review of the patients involved.
"We can reassure the public that all patients have already been treated or are on the appropriate care pathway and undergoing treatment."
He added that the board's internal audit - which looked at a sample of statistics - found no evidence of "deliberate instructions" being given to members of staff regarding the "inappropriate use of waiting times codes".
NHS Lanarkshire also admitted using the "unavailability" classification incorrectly.
But it stated that wrong usage was based on "misunderstandings" rather than any "deliberate manipulation". It added that staff had not reported feeling under pressure to hide breaches or to manipulate data.
