GP leaders have said that general practice would 'grind to a halt' if practices followed the acceptable use policy (AUP) included in an agreement called RA01 that GPs and practice staff in England have to sign in order to obtain smartcards to access NHS IT systems.
Details of the AUP itself were not circulated with the smartcard document, and many GPs signed up without checking to what they were agreeing.
The AUP bans practices from plugging in non-NHS hardware to their computers or installing software without permission.
Dr Mary Hawking, a GP in Dunstable, Bedfordshire, refused to sign RA01 until she had seen the AUP in full.
'The rules mean you can't install any clinical risk assessment tools, audit software or voice recognition software,' she said.
'If you do audits or talks and want to take data home with you on a laptop, you're not allowed to connect a memory stick to your computer to transfer it to a laptop.'
The IT agency is expected to deliver a redrafted version of the policy to a representative of the joint RCGP and GPC IT committee.
Ewan Davis, chairman of the primary healthcare specialist group of the British Computer Society and the joint IT committee lead on the user policy, said the current user policy had been badly adapted from a document created for NHS trusts.
'This was driven by pressure to ensure that smartcards and Choose and Book were up and running quickly,' he said.
'Processes to ensure it happened in line with governance principles were swept aside. It's not the first time this has happened with the IT programme.'
Mr Davis said GPs being asked to sign up to a user policy that was 'nonsense' undermines the principle of good information governance.
'This is a missed opportunity to educate practices about how to handle information,' he said.
However, he welcomed the fact that the joint GP IT committee was being consulted on the new version of the AUP.
Connecting for Health was unavailable for comment.