RCGP chairwoman Dr Clare Gerada said the deadline would probably have to move because the government had yet to set out in detail how the change would be implemented.
She urged ministers to allow GPs to come up with solutions to widening access to practices.
GPC chairman Dr Laurence Buckman agreed that the DoH would 'struggle' to meet the deadline. The GPC was in talks with the DoH to 'help it alter its perception' about practice boundaries, he said.
Dr Gerada said that if boundaries were removed, patients should only be able to choose between GPs in a set geographical area where practices are working together.
County-wide registration would be too broad, but patients could still be free to register across relatively wide areas, Dr Gerada said.
Problems with GP access could be alleviated through better use of technology, such as email consultations, and increased use of pharmacies, she suggested. 'We can make things work. If you leave it, it will work, but within the context of a registered list,' she said. 'If the government stopped interfering and let providers find the answers, we will find them, as we have been doing for 64 years.'
A DoH spokesman said the government still intended to 'press ahead' with removing practice boundaries.
The changes will not feature in the Health Bill but may require an update to the GMS contract, he said.
He confirmed that the DoH was working with GP organisations to resolve 'differences in our position and theirs'.
'There is quite a bit to happen still, but we intend that from April 2012, patients will have a greater choice of GP practice,' the spokesman said.