The fund was launched last week under DoH plans to improve use of new treatments.
But Dr Bill Beeby, GPC prescribing subcommittee chairman, questioned whether it was right to over-rule NICE's decisions on cost effectiveness.
'Is it fair to have an organisation called NICE, which is meant to make that assessment, and then find pressure on the government leads to a special fund for some people?' he said.
The launch came as a report by England's cancer director Professor Sir Mike Richards showed UK use of new cancer drugs lags behind most of Europe.
Sir Mike said the Cancer Drug Fund, launching in April 2011 but starting in interim form from October in England, would help 'several thousand' patients.
But Dr Beeby said it only 'scratched the surface'. 'Cancer drugs can cost £50,000 or more. When you start dividing £50 million by those sorts of figures, it doesn't go far.'
The Alzheimer's Society said Sir Mike's report was a 'scathing indictment of problems with access to dementia drugs' after it ranked the UK 11th out of 14 countries.
Asked why there was no new fund for other disease areas, the DoH said: 'There are some innovative new cancer treatments NICE cannot approve due to cost-effectiveness.
In the long term, the government plans to introduce value-based pricing and make new medicines available to NHS patients.'
