SPOT checks on 41 NHS trusts found three were fiddling waiting list figures and half made mistakes reporting data, the spending watchdog reveals today.
The Audit Commission carried out checks from June to November last year to assess the accuracy of waiting time information within the NHS.
Its report - which may undermine the credibility of Government waiting list figures - found evidence at three trusts of deliberate manipulation of waiting list information.
These were Scarborough and North East Yorkshire Healthcare NHS Trust, East and North Hertfordshire NHS Trust and South Manchester University Hospitals NHS Trust.
At another 19 trusts, there were errors in at least one of the indicators used to assess waiting list performance. They included York Health Services NHS Trust which had errors in two indicators and system weaknesses in two others.
This meant that at 53 per cent of the 41 trusts checked, there was a problem with at least one of six indicators.
Overall, 93 per cent of trusts checked had system weaknesses that gave cause for concern over the accuracy of waiting lists.
South Tyneside Health Care NHS Trust got a clean bill of health in four waiting list categories but were found to have system weaknesses in one area.
Northgate and Prudhoe NHS Trust had errors in four out of five categories.
Some trusts offered appointments at short notice and, when patients could not attend, restarted the waiting time from that day.
Some people were classed as "suspended" but should have been on the active list, and "in extreme cases this included hundreds of patients".
In one case, 2,000 patients were not included on external waiting lists.
James Strachan, chairman of the Audit Commission, said: "This report shows widespread inaccuracy in waiting list figures - some of it deliberate, but also much is due to ineffective management or inadequate systems."
At the three trusts where figures were deliberately manipulated, action has been taken to investigate and tackle the problem, including suspending staff.
NHS chief executive Sir Nigel Crisp said to find three trusts were deliberately manipulating figures was "very disappointing and very sad for the NHS".
The NHS is implementing the report recommendations and trusts where problems were found must report by the end of the month.
By the end of June, all trusts must say how they are dealing with any problems.
The NHS is also making a significant investment in improving information technology, said Sir Nigel.
A spokeswoman for the Scarborough trust said that as their internal investigation was continuing, it would be inappropriate to make any further comment.
John Saxby, chief executive of County Durham and Darlington Acute Hospitals NHS Trust, said like every other trust they would be checking figures.
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