Health minister Mike O'Brien explained that the aim of the policy, which is due for implementation by October 2011, was to put the patient at the centre of primary care.
The initial short mention of the policy within a 30-minute speech was met with a quiet but audible ‘boo' from at least one member of the 1,300-strong audience at Glasgow's SECC on Thursday.
Mr O'Brien's assertion that the RCGP backed the policy was met with incredulity by the audience.
RCGP chairman Professor Steve Field was not commenting on the issue but was expected to mention it in his speech to the conference on Friday.
It is thought that the government might have misinterpreted the RCGP's enthusiasm for tackling the problem as backing for abolishing practice boundaries.
It was the first question that England's health minister faced when he allowed himself to be interviewed by the audience.
Dr Chris Walker, a GP from Wolverhampton, was applauded by the audience when he said: ‘I welcome the emphasis on quality care and resources put into primary care but I'm concerned by the end of practice boundaries within the next 12 months.
‘If we lose practice boundaries, how are we going to visit patients?'
Health minister Mr O'Brien said: ‘The reason we are doing this is not because we believe that large numbers of patients will switch, we don't think that's likely to happen.
‘But some people, particularly young people, who are working in big cities with GPs on the outskirts may want a GP in the centre because that's where they spend most of their time.'
He explained that the RCGP had ‘welcomed the fact that we are moving in this direction' to incredulity from the audience.
Mr O'Brien added above another audible ‘boo': ‘We want to talk this through with the RCGP and professional bodies.'
He said daytime out-of-hours bodies may potentially be able to deliver home visits which were a sizeable distance from new practices.
To laughter, he said: ‘I feel a sense of concern about this all.'
The bulk of delegates GP interviewed after Mr O'Brien's appearance were opposed to the DoH's plan because of the havoc they fear it will wreak on home visits.