In an exclusive interview with GP magazine, Mr Hunt said he did not regret imposing the 2013/14 contract settlement because the NHS had to make savings.
But he added: 'I wouldn't want those changes to the GP contract to be the last word, because I think we need a more fundamental rethink about whether the GP contract is achieving things it set out to achieve in 2004.'
The health secretary said that he wanted to transform GPs' roles, to enable them to deliver more 'personalised care'.
QOF targets could be stripped back to reverse the target and box-ticking culture that 'gets in the way of the personal relationship between doctor and patient', he suggested.
GP reported earlier this year that access would feature in GP contract talks. Mr Hunt said ensuring patients could access urgent and emergency care out of hours may also 'involve changes to the GP contract'.
Changes to the deal could also involve moves to make named GPs responsible for frail elderly patients when they leave hospital.
GPC negotiator Dr Beth McCarron-Nash called for caution and said the profession needed stability. 'The answer to everything is not that we need a new contract,' she said.
Changes such as making named GPs responsible for elderly patients could be enacted through enhanced services, while other improvements depended on moving more funding into general practice, she argued.
'I would like us to have the capacity to provide longer appointments for patients with complex conditions and to see a shift of resources to enable us to have stability and the ability to take on partners and other GPs.'
This year's contract negotiations will be a 'huge challenge', warned Dr McCarron-Nash. 'The whole country is in a challenging economic environment. It is not like they are going to be throwing us pounds.'
She urged Mr Hunt to follow through on his promise of easing GPs' workload. 'Mr Hunt is very good at talking, but last year we had an imposition with worse access,' she said. 'I want to see him walking the walk.'
But BMA council and GPC member Dr George Rae said the current contract had reached the end of its shelf life. 'Now is a good time to look at the contract,' he said. 'We have a new GPC leader in Dr Chaand Nagpaul who is very visionary and it will inevitably be looked at.
'The contract does not fit general practice. It is not right. We have to look at modernising our contract.'