The NHS faces a “big problem” if there are further delays to the timetable for developing clinical commissioning groups or moving to an all foundation trust system, NHS chief executive Sir David Nicholson has told HSJ.

In an exclusive interview, Sir David also revealed he expected the number of commissioning groups to reduce.

Sir David was speaking to HSJ a few days before the government was due to publish a revised Health and Social Care Bill, with health secretary Andrew Lansley promising over 150 amendments. The bill will return to the House of Commons committee stage, before moving on to a potentially stormy passage in the House of Lords during the autumn.

Sir David said he believed there was now “a pretty strong political alliance around the reforms” between the leadership of the two coalition parties and, therefore, he would “be surprised” if “the general thrust of the reforms” was altered.

However, he sent a warning about any further changes which might slow the development of CCGs.

“If that gets disrupted, in terms of timetable, that’s a big problem for us, because a lot of what we need to deliver depends on those GPs engaging and being involved in commissioning, doing the kind of granular changes that are needed to shift care.”

Sir David also rang alarm bells about the move to an all foundation trust system. The blanket deadline of April 2014 for all NHS trusts to have achieved foundation status has been removed, but the government is still expecting that aspiration to be met.

The NHS chief executive said he would also be worried by “anything” that affected the commitment to deliver foundation trusts”.

He explained the foundation trust authorisation process was being used as the “mechanism” to ensure trusts had a “sustainable” future. “If that [commitment] wavers, that’s a big problem for us”, he said.

Sir David acknowledged that controversy over the reforms had been “very distracting” for the service and that the NHS was now entering an “even more difficult” time as reform and savings challenges bit.

“The important thing for me is to draw a line under this period. I know this will be very difficult. But from an NHS leadership point of view, we need to draw a line under it as soon as we possibly can”, he said.

Sir David said it was “critical” for the NHS to focus its attention on the service changes needed to deliver savings in 2012-13 and 2013-14. Those changes needed to be put “in place” during this year, he added.

Sir David is also chief executive designate of the NHS Commissioning Board. He said that “more and more” of the 328 commissioning groups were “talking to each other” and identifying the need to work more closely together.

“The natural way in which people are talking to each other – and the management cost allowance – will reduce the numbers [of commissioning groups] we’ve got.”

He said that details of the management cost allowance for commissioning groups would be revealed in October. The strengthened role of local authority health and wellbeing boards marked a “fundamental” and “radical” shift in the way health services would be run, he said.

Sir David claimed, for example, that the boards would be the place to “negotiate” service reconfiguration and that the input of clinical senates should help ensure very few decisions were referred to the NHS Commissioning Board for review.