THE head of the Scottish health service put pressure on the country's independent watchdog to water down a report on problems with patient waiting times, the Sunday Herald can reveal.

NHS chief executive Derek Feeley pushed Audit Scotland to drop a key phrase which suggested a huge rise in patients classed as unavailable for operations had "disguised" the inability of health boards to meet waiting-list targets.

After Feeley complained about parts of the draft report, Audit Scotland also cut references to official waiting-time figures being incomplete, and "unusual patterns" in waiting-list data.

Feeley, NHS Scotland's chief executive since November 2010, even accused the watchdog of "demonising" the "social unavailability" codes at the heart of the row over waiting times, and demanded that positive statements be inserted in the final report to make it more "balanced".

The waiting-times issue is hugely important to the SNP, as Independence Minister Nicola Sturgeon was Health Secretary in the period examined by Audit Scotland, and any problems would be used by her opponents in the referendum debate.

Social unavailability codes are given to patients who cannot have an operation for non-medical reasons, such as work commitments or going on holiday. This pauses the clock on the patients' guarantee of treatment within 18 weeks of referral to a hospital, and the clock restarts when patients become available again for their operation.

In mid-2008, when the codes came into effect, around 11% of patients received them, but three years later this had almost tripled to 31%.

The surge fuelled suspicions that NHS boards were wrongly marking patients as socially unavailable in order to get them off their books and hit their targets, because fewer patients makes it easier to treat the remaining ones on time.

After it emerged in 2011 that NHS Lothian had indeed been manipulating waiting codes to hit targets, their use mysteriously fell across most of Scotland's other NHS boards, adding to the impression codes had been abused. The misconduct at NHS Lothian and the rise in the codes elsewhere prompted Audit Scotland to undertake one of its most exhaustive inquiries, reviewing around 270,000 patient records.

In its report last month, the auditor said public trust had been put at risk, inadequate NHS records meant it was not possible to say if abuse was widespread, and there was not enough scrutiny of what was happening to patients.

It flagged up unexplained code hotspots – such as 70% of patients at a Glasgow orthopaedic unit apparently being unavailable for social reasons – twice the national average – and the use of the codes leading to under-reporting of patients waiting more than nine weeks for operations.

Using Freedom of Information, the Sunday Herald has now obtained the more damning draft report, and Feeley's comments on it as part of the standard pre-publication clearance process.

On January 29, Feeley wrote to Auditor General Caroline Gardner to flag "six key issues in the draft report which we believe need alteration".

He asked for "greater balance" after Audit Scotland said it could give "no assurance" that manipulation was not widespread. He also asked for a rewrite of the "very strong allegation" that codes had "disguised" failure, and repeatedly objected to any reference to "unusual patterns" in the waiting list data. Audit Scotland agreed to most of the changes.

However, on February 11, Feeley wrote again about "errors of omission", asking for "helpful" points to be added, such as a statement that no deliberate manipulation had been proved, and waiting times were generally falling.

He also complained "about what I can only describe as the 'demonising' of social unavailability in the report", resulting in Audit Scotland's final report stressing the codes had a positive function if used properly.

Labour health spokeswoman Jackie Baillie said: "These revelations take the scandal of NHS waiting times and cover-up to a whole new level.

"This original draft is even more damning for the SNP Government than the one published. No wonder those involved were so desperate to try to tone it down. These targets were put in place so Scottish patients could get the best possible treatment but it appears Nicola Sturgeon and [current Health Secretary] Alex Neil were prepared to collude with NHS bosses to cover up these failings rather than get it right for people."

Scottish LibDem health spokesman Jim Hume added: "This exposes the extremes to which ministers will go to avoid criticism. Patients want lessons learned from this scandal. They don't want Government ministers and their appointed chiefs airbrushing the problems away."

Mary Scanlon, Tory deputy of Holyrood's public audit committee, which recently quizzed Feeley about waiting times, said the material raised new questions, and accused SNP MSPs of trying to "close down any potential criticism that might be levelled at the SNP Government".

The Government stressed Audit Scotland made the final decision on what appears in its reports. A spokeswoman said: "In line with standard procedure, Audit Scotland asked us for comments on the draft report. In the interest of accuracy, Audit Scotland accepted a number of our points and amended the final report accordingly, in exactly the same way as has been done on many other occasions. As the Auditor General has made clear, Audit Scotland found no evidence of dishonest manipulation of waiting times."