Sir David Nicholson will remain NHS chief executive for the whole of 2012-13, as well as leading the NHS commissioning board in its initial stages, the Department of Health has revealed.

The measure is revealed in the Department of Health’s new command paper on NHS reform which sets out planned changes to the Health and Social Care Bill. The document says: “Sir David Nicholson will retain his current role as NHS Chief Executive for the whole of 2012-13, alongside his role as chief executive-designate of the NHS Commissioning Board.

“This will help ensure that all parts of the system are fully aligned during the shift to the new structures.”

The NCB will be set up in shadow form in October 2011, and will be established as an independent statutory body in October 2012, when it will begin carrying out some functions, such as authorising clinical commissioning groups.

The board will become fully operational from April 2013.

The command paper, which forms the official government response to the NHS Future Forum’s report on the health reforms, confirms a relaxed timetable for the controversial restructure of the service.

Strategic health authorities will be abolished in April 2013, a year later than originally planned. Primary care trusts will also cease to exist on that date, but clinical commissioning groups will only take over full commissioning duties where they are “ready and willing”.

The paper said the “greatest concerns” they had were about the timetable for moving to the new system of clinically-led commissioning, and that some groups would not be able to take on some or all of their duties in time for the original April 2013 deadline.

Now, GP practices will be members of either an authorised CCG or a shadow group by that date.

Where a CCG has not taken on full budgetary commissioning responsibility after April 2013, a local arm of the NCB, based on primary care trust clusters, will commission “on its behalf”.

The paper says ministers “strongly expect that the majority of remaining NHS trusts” will be authorised as foundation trusts by April 2014. While “it will not be an option” to remain as an NHS trust, there will be no “blanket deadline” for achieving foundation status.

The principle of Any Qualified Provider will be established “in a phased way”, starting in April 2012, and focused on services “where patients say they want more choice”.

Monitor will retain specific oversight powers of FTs until 2016.

HealthWatch England and local HealthWatch branches will be established in October 2012.

The paper says: “Drawing on concerns [the NHS Future Forum] heard, we accept the need for more flexibility, to recognise that some organisations may not be ready to take on their full responsibilities, or perform at full capability, on the current timetable – while allowing those who are ready to make faster progress, in line with the current pathfinder programme.”

The paper also reveals that the Department of Health has asked the NHS Future Forum to “continue to advise the government on how the transition can be managed successfully”.

Further detail on the timetable for transition will be set out in a forthcoming letter from Sir David Nicholson to NHS organisations.