The RCGP launched a petition last week demanding guarantees that GP trainee pay would not be cut under the imposed junior doctors' contract.
College chair Dr Maureen Baker said Jeremy Hunt had pledged not to undermine GP trainee recruitment, but called for greater clarity on how junior doctor pay changes would affect them.
Talks between the government and the BMA junior doctors committee broke down last month over doctors' fears the deal the government was seeking would put patients at risk.
Junior doctor industrial action
The committee has refused to re-enter talks unless the government withdraws plans to impose a new contract and gives guarantees over recognition of antisocial hours as 'premium time', pay for all hours worked and 'hours safeguards' to protect doctors and patients.
BMA junior doctors committee chair Dr Johann Malawana said: 'Today’s decision is a reflection of the anger felt by the thousands of junior doctors who have told us that the government’s position is not acceptable.
'The BMA has been clear that it wants to deliver a contract that protects patient safety and is fair to both junior doctors and the health service as a whole. We can only do this if the government is prepared to work collaboratively in a genuine negotiation. Unfortunately, they have chosen to ride roughshod over the concerns of doctors with their threat of imposition.'
Speaking at the Labour party conference in Brighton, shadow health secretary Heidi Alexander said: 'There are problems across the whole NHS with workforce.
'Nobody wants to see industrial action. But equally nobody wants to see junior doctors who are so exhausted they can't provide safe care. My understanding of the current situation is that the government have made a whole series of demands across a whole range of issues and the doctors don't feel the government are in effect negotiating in good faith. So I think Jeremy Hunt needs to show he is willing to compromise, that he is willing to come back with a better deal.'
A DH spokeswoman said: 'It’s disappointing that the junior doctors’ committee has decided to ballot for industrial action in advance of receiving a formal offer from the government. We urge the BMA to reconsider this decision and come back to the table because there is a great deal to discuss about how we reward the profession.
'We are not cutting the paybill for junior doctors, and want to see their basic pay go up just as average earnings are maintained. We really value the work and commitment of junior doctors, but their current contract is outdated and unfair - the best way of changing that is negotiation.'