The 2007 GP Systems of Choice (GPSoC) deal, which secured the provision of IT systems from a range of suppliers, expired in April 2013.
NHS England extended the existing arrangements when the deal ran out and had expected to complete a replacement agreement by the end of 2013.
But the deal has been delayed again and is now expected to be completed in March.
NHS England said although it had expected the new deal to be in place by the end of 2013, the 19 shortlisted firms for the core element of the new GPSoC contract were only asked to submit detailed proposals on 15 January 2014.
A spokesman for NHS England said the reason for the delay was an extension to the scope of the framework and a higher than expected number of bidders.
The new GPSoC contract is divided into three lots. Lot one is the core contract, for which there were 57 bidders.
Past chairman of the British Computer Society Primary Healthcare Specialist Group, Ewan Davis, said the uncertainty was not ideal for GPs, but the number of bidders for the contract had been surprisingly high.
EMIS National User Group secretary Dr Paul Maddy said: 'Although it has taken longer than originally envisaged to complete the new framework agreements, the GPSoC team has ensured that the existing framework has been rolled forward, so that practices could continue using their current GPSoC clinical systems without any concern.
'The GPSoC team has kept all of the user groups fully informed of the progress towards completion of the new GPSoC-R framework agreement.'
The GPSoC-R deal, which stands for 'replacement', will 'help strengthen links between clinical suppliers and their user groups', Dr Maddy said. He added: 'User group members will have opportunities to influence the development of their respective clinical systems.'
A BMA spokesman said: 'We are satisfied that the interim measures put in place to extend the previous programme are satisfactory and ensure the continuity of GPSoC entitlements for practices.'
The NHS spokesman added: 'There is no action required by GP practices regarding the GP systems they currently use. We will communicate operating arrangements to GPs through a number of channels as and when appropriate.'