In a statement to parliament on Wednesday, Mr Hunt said that the government and the NHS had been left 'in no man's land' after junior doctors voted to reject a deal struck between NHS Employers and BMA negotiators.
The health secretary hit out at BMA tactics in 'over three years' of talks on a new deal for junior doctors, and accused the union of having 'stirred up anger among its own members it is now unable to pacify'.
BMA junior doctors committee chairman Dr Johann Malawana resigned on Tuesday after 58% of junior doctors voted against a contract that he had recommended as a 'good deal' that was the 'best and final way of resolving this dispute'.
Junior doctor strikes
Mr Hunt paid tribute to Dr Malawana, but said that following his resignation it was not clear that anyone in the BMA could deliver the support of members for a negotiated settlement.
The health secretary told MPs that the contract deal struck between the BMA and government negotiators in May was 'a historic agreement on a new contract for junior doctors after more than three years of negotiations and several days of damaging strike action'.
He admitted the deal helped the government to deliver on its manifesto commitment to a seven-day NHS, but added that the deal did 'much more' - citing a reduction in the maximum hours junior doctors can be asked to work, child-friendly rostering and support for women who take maternity leave.
'Unfortunately because of the vote we are now left in a no man's land that if it continues can only damage the NHS,' Mr Hunt said. 'An elected government whose main aim is to improve the safety and quality of care of patients has come up against a union which has stirred up anger among its own members it is now unable to pacify.
'I was not a fan of the tactics used by the BMA but to its credit its leader Dr Johann Malawana did in the end negotiate a deal and work hard to get support for it. Now he has resigned it is not clear that there is anyone able to deliver the support of BMA members for any negotiated settlement.
'Protracted uncertainty at precisely the time we grapple with the enormous consequences of leaving the EU can only be damaging for those working in the NHS and on the patients who depend on it.
'I have this morning decided that the only realistic way to end this impasse is to proceed a phased implementation of the exact contract that was negotiated, agreed and supported by the BMA leadership.'
Deciding to impose the deal had been 'difficult', but different groups of junior doctors will move to the new contract in phases up to October 2017, the health secretary confirmed.
He said the deal was better for the NHS and junior doctors than the deal the government originally planned to impose in March.
Shadow health secretary Diane Abbott said the NHS was only as strong as the morale of its staff, and warned that the rejection of the contract deal showed morale was at 'rock bottom'. She urged the government to reconsider its decision to impose the deal.