Lord Howe's comments came in response to the BMA's first formal response to the 2013/14 GP contract proposals, published on Monday.
A letter from GPC chairman Dr Laurence Buckman set out its opposition to plans for the QOF, and said these would have 'serious implications for patients and practices'.
In response, health minister Lord Howe said: 'Improving patient care is our priority. We want to make sure the best possible care is provided in a more consistent way across the country.
'Our changes aim to help GPs manage their workload at the same time as making improvements which will mean better care for all - especially patients with long-term conditions and dementia.
'We believe GPs can and will rise to these new challenges.'
The GPC said it had chosen to publish its response to the clinical elements of the GP contract proposals first because the plans are 'complex' and will need to be planned for 'well before April'.
The consultation on the GP contract will end on 26 February.