Slough CCG and Northumberland CCG have both written to the DH demanding 'fairer' funding allocations.
The head of Northumberland CCG, Dr Alistair Blair, has made 'formal representations' to the DH and 'senior health advisers within government' about the allocation formula for health and rural populations.
The financial situation in Northumberland was described as 'challenging' in the minutes of the NHS North of Tyne board meeting last month.
Slough CCG in Berkshire has also asked the DH for more money. Dr Gurdip Hear, one of the four directors of the group, said: 'It is unfair as we are getting less than inner-city areas. But we are more deprived than other areas.'
GPC deputy chairman Dr Richard Vautrey said patients could suffer if any change in the funding formula was brought in quickly. 'It was inevitable that a change in the funding allocation for CCGs would lead to winners and losers, and if it is implemented poorly, the losers will be patients,' he said.
'We would want to see the rationale for any change before it is implemented and if there is evidence for such a change in allocation, it should then be implemented slowly to allow for areas to make the necessary plans to adjust.'
The DH has announced estimated CCG allocations, based on £25 per patient per year including unregistered patients.
But a DH spokesman said no decisions had been made and the Advisory Committee on Resource Allocation would publish its recommendations on resources for CCGs 'shortly'.
'We are making sure that funding is given to areas that need it most,' he said.
'Independent experts are providing advice on how best to achieve this. No decisions have been made.'