There are concerns that primary care trust benchmarking decisions and information on patient numbers, which informs payment by results, may be out of date as third quarter results (October-December 2006) were not published until mid-May.
A source at a data management service revealed that third quarter data was due in April but had been delayed by 'various data quality issues'.
It has emerged that some trusts have experienced problems in submitting statistics since the data collection hub - the NHS-wide clearing system - was replaced with the secondary uses service at the end of December.
This appears to have caused delays in the processing of the first statistics extracts because some hospital patient administration systems have been incompatible with new software, meaning some extracts are missing from the latest dataset.
Paul Robinson, external relations manager of independent health service information provider CHKS, said he knew of trusts that had experienced this problem.
Others, he said, had faced delays because they were waiting for new third party software to be accredited. An information manager confirmed this was the case at his Midlands trust and said that the hospital had supplied its episode statistics direct to its PCT, bypassing the secondary uses service, to avoid further delays.
Mr Robinson also said he was aware of some hospitals submitting data under both old and new PCT codes, resulting in duplication of records. 'Even if the data is published now it is still significantly out of date information to be basing benchmarking on,' he added.
Dr Paul Aylin, assistant director of the Dr Foster unit at Imperial College London, said: 'We have certainly heard there are some issues with the third quarter data.
'If you're missing records this will impact on benchmarking and payment by results. If you don't have up-to-date information then the whole issue of charging becomes difficult.'
Information Centre for health and social care operations director Roger Dewhurst admitted: 'A minority of NHS organisations have had difficulties in submitting the necessary data over the last few months.
'As a result of the reorganisation of PCTs in October last year, some organisations used incorrect PCT codes to correct previously submitted data. This resulted in a higher number of duplicate patient activity than usual. These have been removed from quarter three statistics and organisations are correcting this through re-submissions.'
Organisations will be able to correct any inaccuracies until mid-June before the final set of annual data is published later this year, Mr Dewhurst added.