The plans have raised concerns that patient care could be compromised by linking GP pay to cost-effectiveness, such as through further incentives for generic prescribing.
But new indicators will not be imposed, according to NICE chief executive Andrew Dillon.
Mr Dillon said that once NICE had tested the clinical and cost-effectiveness of indicators, contract negotiators would decide how they would be introduced into framework payments.
He said the DoH wanted economy of use of NHS resources to feature in GPs' pay and suggested a go-ahead to start work on new indicators was a formality.
NICE's updated indicators could take effect from 2010. 'The indicators that are selected both have the effect of improving quality of care and ultimately the outcome for the patient ... and make the best use of NHS resources,' Mr Dillon said.
But linking more of GPs' pay to cost-effectiveness will not necessarily promote best use of NHS resources, Dorset GP Dr Graham Archard warned.
He said medicines prescribed generically were often unused because patients received different versions at different pharmacies and did not take them because they were not used to the appearance or taste.
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