Some PCTs will miss the April 2011 deadline for transferring their provider arms, it warned last week.
PCTs that have not already decided on future options for their provider arms will not be able to transfer them in the next six months, the confederation warned. It said PCTs may be making decisions to fit the tight timetable, rather than making the right decision.
In a briefing paper on community services reforms, the NHS Confederation also said the 'any willing provider' policy may disrupt newly established or merged community services.
It added that IT systems used by community services may not work with systems in trusts they are transferred to and that GP commissioning presents a further challenge.
It said: 'Community services staff have a complex relationship with GPs. Many practices consider community frontline staff as "theirs" and will want to have a say in any proposed changes to current arrangements.'
Meanwhile, the NHS Confederation also warned that transferring services to other NHS providers or converting them into social enterprises without transforming how they work is a waste of time, effort and 'considerable resources'.
David Stout, director of the NHS Confederation's PCT Network, said: 'We must not forget that in the midst of these changes, NHS organisations still need to make significant savings. These services must be able to truly transform the way patients receive care while at the same time doing more for less money. If this is not achieved on a broad scale, all we will have is another expensive reorganisation of services.'