A DoH spokesman said that although the GP systems of choice (GPSoC) framework expires in August, practices will continue to receive IT support and services until the end of March 2013.
Meanwhile, health IT consultant Ewan Davis - a former joint RCGP/GPC IT subcommittee member, urged the DoH to hand responsibility for IT commissioning to consortia.
The DoH said extending the GPSoC deal would give practices continuity of services during the NHS reforms.
GPC negotiator Dr Chaand Nagpaul said the move was a 'sensible arrangement' that provided security for practices' IT systems.
He said: 'Even though there are significant reorganisations taking place in the NHS with PCT clustering, GPs need to be aware that they have the same entitlements for support for IT systems as before.'
Clarity on the role of GP consortia
Dr Nagpaul said the GPC was in talks with the government about arrangements to put in place after March 2013.
'The extension of agreements to 2013 allows breathing space for us to have a meaningful dialogue with the DoH for arrangements after 2013,' he said.
'This will depend upon greater clarity regarding the role and functions of GP consortia and the NHS Commissioning Board.'
Meanwhile, Mr Davis said IT commissioning responsibility must be handed to consortia, as handing it to the NHS Commissioning Board would be a 'dreadful outcome'.
He said: 'If we move it to consortia that would be a very welcome change. It would give GPs more influence over the IT they want and need and drive innovation.
'Giving IT responsibility to the NHS Commissioning Board at a national level will mean IT services are unresponsive to the local needs of GPs.'