BMA leaders have repeatedly called for prescription charges to be abolished across the UK.
But a survey of 1,266 GPs found that 63 per cent do not support the move. Just 32 per cent do, while 4 per cent remain unsure about the issue.
GPs suggested that providing free prescriptions to all patients would be unaffordable.
Many argued that well-off patients should not qualify for free prescriptions, even if they had long-term conditions.
'Patients should bear part of the cost of any medication or treatment, so they understand that these things are not free,' one said.
Prescription charges were abolished in Northern Ireland last week and cut to £3 in Scotland, where they will be scrapped next year.
Charges were abolished in Wales in 2007. But in England they remain at £7.20.
The BMA believes that abolishing prescription charges is the 'fairest and the simplest' way to overhaul a system which is 'outdated, iniquitous, and detrimental to the health of many patients'.
The GPC restated its support for the removal of charges in its annual report last month.
But 58 per cent of GPs back ending prescription charges for patients with long-term conditions, the survey found.
Gordon Brown announced in 2008 that he would scrap charges for patients with long-term conditions. But the government's review on the issue has never been published.
GPs are split on whether prescription charges prevent people accessing healthcare.
In total, 50 per cent believe charges do represent a barrier to health treatment. 'For some the costs mean they do not get their medicines,' one GP said.
However, 47 per cent of GPs said charges do not block access and 3 per cent are unsure.
A number of GPs called for increased publicity for prepayment certificates. 'Prepayment certificates are the fairest way of protecting those on multiple medicines,' one argued.
Others suggested a small fee of around £1 on all prescriptions to limit frivolous use.