Iain Duncan Smith has accused the government of having a "culture of fiddling the figures" on NHS waiting times.

The Conservative leader called on Tony Blair to apologies to patients hit by "political meddling" in the running of the health service.

He was speaking in the Commons after an Audit Commission report revealed evidence of waiting list manipulation in three NHS trusts.

Duncan Smith said the government had failed to take action to address the problem, despite being warned about it 15 months ago.

The prime minister said that it was important to have targets for the health service, adding that "it is the desire of the Conservative Party to run down the National Health Service because it wants to cut its funding".

Amid controversy over the findings, NHS managers said the health service should not be judged on the sole basis of the report.

The Audit Commission said that while its investigation had found evidence of incorrect waiting lists in three NHS trusts, all had taken prompt action to investigate and deal with the issues identified, including the suspending of staff.

Auditors completed spot checks at 41 trusts last year and found evidence of reporting errors in 30 per cent of performance indicators.

Just three trusts were given a clean bill of health, with no significant problems found in their reporting systems.

In the other trusts, auditors concluded that weaknesses in the systems increased the risk of errors in at least one performance indicator.

Responding to the report, the NHS Confederation said that any manipulation of waiting lists was "clearly unacceptable" and breached the new code of conduct for NHS managers.

But it pointed out that the 41 trusts examined in the report had been selected specifically because they were hospitals where problems were most likely to occur.

"We must not condemn NHS management on the basis of the actions of a small minority of trusts," said chief executive Dr Gill Morgan.

The report found that in the majority of cases the inaccuracies in the waiting lists were unlikely to have affected the care of individual patients.

But it added that some practices that comply with Department of Health guidelines - such as offering appointments at short notice and restarting waiting times if patients cannot attend - would be considered unreasonable by patients.

Poor management arrangements for recording data and ineffective or poorly integrated IT systems were blamed for the systemic weaknesses.

And the report urged ministers to investigate why there has been widespread misreporting, make changes to the process for patient cancellations and be clear how changes in clinical practice should be reflected in waiting lists.

"This report shows widespread inaccuracy in waiting list figures - some of it deliberate, but also much of it due to ineffective management or inadequate systems," said Audit Commission chairman James Strachan.

"Some trusts have lost sight of the real priorities, which are about improving the NHS for the patient not just meeting government targets.

"At the same time the management and systems of the NHS in this area clearly require significant improvement."

The NHS Confederation also accepted that there was a problem with "under-valued junior staff all too often struggling with poor guidance and a legacy of years of under investment in information systems".

The suspension of employees at three NHS trusts, prompted by the Audit Commission investigation, also led to concern that the process followed in internal investigations did not conform to agreed disciplinary procedures.

NHS chief executive Sir Nigel Crisp said that any deliberate mis-reporting of waiting list data was "absolutely inexcusable".

He warned of "serious consequences" for any individual or NHS organisation that fraudulently manipulates their performance data.

"Deliberate mis-reporting of waiting list data is reprehensible and inexcusable and we have made it very clear that serious consequences will follow any individual or trusts that seek to manipulate their performance data," he said.

"The code of conduct for managers sets out very clearly that it will not be tolerated. Disciplinary action has followed at the trusts where deliberate manipulation of the figures was confirmed."

But union representatives warned that disciplinary procedures could be flawed.

The FDA, which represents senior managers and professionals in public services, highlighted the need to establish an acceptable process to deal with the issues raised.

Paul Whiteman, head of the FDA's health section, said the process followed in internal investigations of this type did not conform to the rigour demanded by agreed disciplinary procedures.

"The outcome is that managers' careers are being destroyed without them being afforded the right of a fair procedure. Those affected are not able to put their interpretation to thefull investigation team and have no right of question and reply," he warned.

"This report raises some very serious concerns about the actions of some, but it goes on to make accusations and conclusions that do not appear to be supported by robust evidence."