Prodigy, a tool embedded in GP IT systems until last month, was removed because the contract for its use was to end in April and it was no longer being updated.
It offered diagnosis and treatment protocols for GPs to follow in consultations, and prescription information for patients.
But GPs who used Prodigy say its removal has increased consultation times because no replacement is available.
Sir Muir Gray, responsible for this part of the national IT programme and a director of the National Knowledge Service, said a tool had been commissioned to replace Prodigy.
But he added: ‘I would consider putting Prodigy back if the replacement cannot be embedded in GP IT systems within a reasonable period of time.’
The Sowerby Centre for Health Informatics, in Newcastle, developed the Prodigy system and last year won the contract to replace it.
The new service, Clinical Knowledge Summaries, will provide decision-support information based on NICE guidance and research evidence. It will convert all Prodigy guidance to a new format by 2009.
Prodigy user Dr Daniel Albert, a Leeds GP, said: ‘I use it for more than half of my prescriptions. It produces detailed prescription information for patients.’
He said prescribing quality would suffer without a tool like Prodigy because GPs did not have time to type detailed instructions.
He added that the protocols GPs had to go through when using Prodigy promoted clear thinking.
However, some GPs welcomed the withdrawal. GPC IT subcommittee chairman Dr Paul Cundy said: ‘Prodigy has never been used by more than 10 per cent of GPs, so it should not draw on NHS IT funding.’