Although the paper had been available on the NHS website for several weeks, it was withdrawn from the NHS National Electronic Library for Health a day after Computer Weekly questioned the Department of Health about points raised by the paper.
The department said the paper had been withdrawn last week because "it is still in the process of review".
The intention of the management paper was to brief NHS managers on government plans for IT-led reforms and what the strategy would mean to them. The paper supported the objectives of the plans and urged managers and clinicians to become involved in the national programme for IT (NPfIT) - a strategy to introduce electronic health records, e-prescriptions, online appointment booking and a new technology infrastructure.
The paper said the NPfIT had adhered well to its declared timetable but added that within the Department of Health's overall IT plans, and within the NPfIT, there were "perceived to be numerous significant problems and weaknesses".
Its wide-ranging criticisms of the way the NPfIT is being implemented - many of which echo those raised by Computer Weekly - included a lack of clarity about local NHS trusts' funding levels and a concern that insufficient attention had been paid to the cultural and organisational issues. The paper also said the timetable for implementing the NpFIT was "very tight", and warned that this could mean that IT systems would not be adequately tested.
Another concern was that insufficient effort had been made to involve some medical groups and clinical specialities when drawing up plans for the Integrated Care Records Service. This service is designed to implement Tony Blair's plan for every patient to have an electronic health record by the end of 2005.
The briefing paper went on to say there were concerns about the quality of data that would be included on a national data spine of personal health information. The spine is due to go live by the end of next year.
The paper was written by Catherine Ebenezer, a former NHS librarian and now IS manager at the Royal College of Midwives. She declined to comment on its withdrawal.
Computer Weekly put to the NPfIT all of the 13 points which were listed as significant problems and weaknesses.
A spokesperson for the NPfIT replied, "The national programme has made efforts to view the management briefing paper submitted to the NHS National Electronic Library for Health website that covers areas relating to the NPfIT.
"It understands that the report in question is currently unavailable as it is still in the process of review. In the absence of access to the full text of the paper and the context of the references to the national programme, it is unable to comment at this time."