A DoH spokesman admitted GPs have concerns about the proposals, but it said it was working to address them.
He said the DoH still aims to give patients 'far greater choice of GP practice' from April next year.
It comes as the Patient Association said the government must follow through with its promise for greater patient choice in the NHS.
It raised concerns that many patients have difficulty registering with a practice close to where they live and said that many other patients would prefer to register with a practice close to their work.
Celia Grandison-Markey, interim chairwoman of the Patients Association said: ‘For years we have been told that patients will be allowed to register with any GP even if they live outside the practice boundaries yet we are still waiting for this to happen.
‘The Government has promised patients choice in the NHS, and the removal of practice boundaries and they must honour this.’
The RCGP said that it is not against patient choice on GP registration. But it warned that removing practice boundaries would ‘seriously affect’ the safety of vulnerable patients, put rural practices at risk of closure and create difficulties with home visits.
RCGP chairwoman Dr Clare Gerada said: ‘GPs want patients to have good-quality, accessible primary care services close to home. Patients want to be seen by health professionals they know and trust who will share decisions with them around their care.
‘The RCGP is confident that the small number of patients who commute long distances and who would like to access a GP close to their place of employment could be accommodated through greater access to walk-in centres, or telephone and electronic consultations with a GP.’