IN opposition Nicola Sturgeon campaigned effectively to end what she called the scandal of "hidden waiting lists" in NHS Scotland.

Under the old system thousands of patients – a staggering 35,000 at the peak – were removed from the headline waiting lists if they were unable to attend an appointment, unfit for treatment or simply regarded as a low priority. In the jargon of the health service they were given an "availability status code".

The focus on hidden waiting lists and Labour's failure to bring down the numbers quickly enough helped lose them the 2007 election.

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So there was backing from all sides a few months later when Ms Sturgeon, by now installed as Health Secretary, declared: "This new SNP Government will do in our first year what the last government failed to do in eight years – ensure that hidden waiting lists in our NHS are a thing of the past." The system she brought in did away with availability status codes and introduced a "personal waiting time clock". If, and only if, a patient was genuinely unavailable for treatment would the clock stop. It would start ticking again when they became available.

Labour said it had been planning to do it all along.

But four years on the system is being changed again. A series of internal health board audits published this week suggested the clocks were stopped for all sorts of reasons as the NHS struggled to meet Government waiting time targets.

In NHS Lothian, where concerns first emerged late last year, patients were offered short-notice appointments in England and marked "unavailable" if they could not attend. In Grampian and Tayside, patients were told they might not be treated on time and were recorded as unavailable if they agreed to a delay. Coupled with figures showing the overall number of patients declared "socially unavailable", they suggest widespread abuse.

The total was running at 17,000 when the NHS Lothians scandal broke but since then it has nearly halved. Major falls were recorded in all of Scotland's mainland health board areas.

For Labour's health spokeswoman Jackie Baillie, this shows that boards, alarmed by the backlash over NHS Lothian, looked again at their own practices and suddenly become much more cautious about declaring people socially unavailable. The suggestion is that health boards were routinely cooking the books and only stopped when NHS Lothian was rumbled.

Fiddling the figures does not mean patients' treatment is being deliberately delayed.

Not necessarily, anyway. Declaring people "socially unavailable" buys health boards time in terms of the waiting time guarantee and it's possible they could take advantage of that.

But the limited internal audits provide no hard evidence that has been happening. Unless proof does emerge, it is only be fair to assume that health boards are treating people as quickly as they possibly can – just not as quickly as they have been claiming.

The scandal lies in saying the all-important 18-week waiting time guarantee is being met when the reality appears to be quite different for thousands of patients.

This takes the issue to the heart of government. Comments in the NHS Tayside report reveal the intense pressure placed on boards to meet the waiting target. Staff said they felt bullied into marking patients unavailable.

The SNP administration has trumpeted its record on health. Ministers have chosen to protect the NHS budget more than anything else from deep spending cuts across the public sector, so the pressure is on to deliver. Regular press releases have highlighted good news on waiting times. But if the reality is different, it will be a major embarrassment. All eyes will be on Audit Scotland's comprehensive report on waiting times when it is published early next year.