A DoH spokesman admitted GPs had concerns about the proposals, but it said it was working to address them.
But he said the DoH still wanted to give patients 'far greater choice of GP practice' from April 2012.
The announcement came after the Patients Association said the government must follow through with its promise for greater patient choice.
It said many patients had difficulty registering with a practice near where they live and 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 was 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: '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.'
Last week, the annual conference of LMCs backed a motion calling on the GPC to resist the government's plans to remove practice boundaries.