NICE has expressed disappointment that the GPC and DoH decided not to include the indicators it reviewed and developed in next year's QOF.
But the institute said it will now look at how to 'make best use of the valuable work undertaken'.
The DoH has said that primary care organisations could use NICE-approved indicators to improve the clinical and cost-effectiveness of the services they commission through LESs.
NICE proposed new indicators for epilepsy and Down's syndrome, along with revised indicators for BP in diabetes. However, as part of the agreement on payment for the swine flu vaccination programme, it was decided that no changes should be made to the 2010/11 QOF.
David Stout, director of the NHS Confederation's PCT Network, said PCTs would welcome the ability to use the indicators as LESs.
'The fact that they have been assessed by NICE is good,' he said. 'We have argued in the past about the benefits of using incentives to improve care and these would fit into that.'
'If PCTs thought there was better evidence and better indicators in those issued by NICE than the LESs they already have, they could move to those developed by NICE,' Mr Stout said.
However, he added that it was not clear where the resources would come from to pay for additional LESs.
NICE is expected to announce further details of how it might support development of indicators in the future.