College chairwoman Dr Maureen Baker met health secretary Jeremy Hunt on Monday to discuss the dispute.
The BMA began balloting junior doctors over strike action last week after the government threatened to impose contract changes.
Junior doctor contract
The proposals would increase juniors’ standard hours before overtime, remove automatic pay progression and limit working hours.
Mr Hunt has pledged that GP trainees will not lose out under the reforms, despite plans to scrap the existing GP training supplement.
Dr Baker said: ‘It was a useful meeting in which I had the opportunity to reiterate to Mr Hunt that the RCGP supports our junior doctors wholeheartedly – and how crucial it is to reach a speedy resolution.
‘I urged the health secretary to call in the independent negotiators and abandon any pre-conditions to the contract so that talks can re-start, in the best interests of our doctors and our patients.
‘We also discussed GP recruitment and the government’s acknowledgment that general practice is now a shortage specialty.
'We have received no threats whatsoever over the future of our royal charter and the issue did not come up.
‘The college has no influencing power over the negotiations, which are the remit of the BMA.
‘But, as the UK’s largest medical royal college representing over 50,000 family doctors, we are extremely concerned that the ongoing disagreement between the government and junior doctors threatens to destabilise the NHS and poses a risk to safe patient care.
‘It has badly hit morale across the NHS at a time when we should all be working together to prevent our health service from tipping over the edge, particularly as we head towards what will be a very difficult winter for our general practices and hospitals.
‘Junior doctors choose medical training because they want to care for patients and contribute to the NHS. They should be allowed to do this without fear for their own financial futures and the safety of generations of patients who will be reliant on them.’