NHS Connecting for Health and SHAs are still working through the details of the local ownership programme (NLOP) a fortnight after the 1 April deadline for transfer of the main responsibilities passed.
The process, which will devolve parts of the national IT programme to SHAs, has entered a 'transition period' and now looks unlikely to take place in full before July.
A 'transition assurance review' is being carried out to assess the risks the delay might pose to the successful delivery of the IT programme.
NHS Yorkshire and the Humber chief information officer Phil Molyneux said key details such as funding were yet to be finalised.
'A number of responsibilities have been transferred but there are still some policies and processes that need to be signed off,' he said.
A recent NHS South East Coast board paper confirms that 'complex negotiations are continuing' over NLOP. It adds: 'The initial intention was to make the substantive changes in April. The process is now running more slowly, with a view to transferring responsibilities and staff to SHAs by July.'
NLOP was launched in October to make SHAs more accountable for delivery of the programme.
It followed a National Audit Office report last year that said a critical factor in the IT programme's success would be the support of NHS staff.
CfH will continue to take responsibility for areas such as commercial strategy and contracts with suppliers. The SHAs, working with trusts and PCTs, are to take over local delivery and implementation of products.
'We'll be failing the public of this country if we don't find ways of using all this extra investment going into IT to transform services,' said Mr Molyneux. 'There are lots of areas where we should have made an impact but haven't.'
But there have been concerns over whether NLOP will provide genuine local control or just shift accountability away from CfH. Although SHAs took on this extra accountability on 1 April as planned, their full responsibilities are yet to be confirmed.
Director of service implementation Richard Evans said: 'The transition to local ownership involves a lot of detailed discussions between many parties. It's important to get these discussions right and they have taken longer than originally planned. However, all parties are working together to complete them successfully over the coming months.'