The findings undermine the case for DoH plans to push GPs to move into polyclinics and supersurgeries.
Statistics from the Improving Practice Questionnaire (IPQ), which asked patients at 2,500 practices for their views, show that satisfaction levels are higher when a practice is smaller.
In 2006/7, UK practices with a list size below 3,000 achieved an average satisfaction score of 68 per cent, compared to 63 per cent for practices with 6,000 to 12,000 patients and 61 per cent for those with more than 12,000.
The most marked differences in patient satisfaction between small and large practices relate to telephone and 48-hour access, the ability to see their first choice of practitioner and waiting times.
Dr David Jenner, clinical director at IPQ's analysts CFEP UK Surveys, will submit the findings to health minister Lord Ara Darzi, who is carrying out a national NHS review and is known to back larger practices.
Lord Darzi's review of NHS services in London earlier this year recommended the use of polyclinics across the capital.
Dr Jenner said: 'These figures show there are aspects of small practices that patients value. We need to look at the implications of that before we redesign the NHS.'
Dr Jenner said the survey added weight to the RCGP's calls for a 'federated model', in which practices work collaboratively instead of merging.
Dr Michael Taylor, chairman of the Family Doctor Association, formerly the Small Practices Association, said: 'These figures are consistent with all the recent data about patient satisfaction and practice size.
'The DoH talks of a patient-led NHS, then develops policies that ride roughshod over small practices.'
He said the data were 'excellent ammunition' for small practices.
GPC chairman Dr Laurence Buckman, a single-handed GP, was worried that ministers would ignore evidence that patients favoured smaller practices.
'This government operates in an evidence-free zone. I hope Lord Darzi will take it on board and insist that the DoH operates policies based on evidence, but I fear it will not,' he said.
A DoH spokesman said: 'DoH policies are grounded in evidence. GPs themselves are choosing to group together in bigger practices.'
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