The vote is a devastating blow to negotiators from both sides who had hoped that a deal struck through the mediation service Acas could finally draw a line under a dispute that had sparked a wave of unprecendented strikes by thousands of junior doctors.
A total of 58% of junior doctors voted against the new contract and 42% in favour, on a turnout of 68% - around 37,000 junior doctors and medical students.
In a statement after the referendum result, Dr Malawana said: 'The result of the vote is clear, and the government must respect the informed decision junior doctors have made. Any new contract will affect a generation of doctors working for the NHS in England, so it is vital that it has the confidence of the profession.
Junior doctor strikes
'Given the result, both sides must look again at the proposals and there should be no transition to a new contract until further talks take place.
'Having spoken to many junior doctors across the country in recent weeks it was clear that, while some felt the new contract represented an improved offer, others had reservations about what it would mean for their working lives, their patients and the future delivery of care in the NHS. There was also considerable anger and mistrust towards the government’s handling of this dispute.
'These concerns need to be fully addressed before any new contract can come into effect and, in light of the result, I believe a new chair will be better placed to lead on this work.
'There is much to do to in order to rebuild the trust that has been eroded over the last year. The government must now do the right thing, accept the outcome of this vote and work constructively with the BMA to address junior doctors’ concerns with the new contract.'
Junior doctor contract
NHS Employers chief executive Danny Mortimer said: 'I am profoundly disappointed the BMA has rejected the proposed new contract for junior doctors. It is imperative that patients will not be made to suffer any further impact as a result of the rejection of the contract.'
Health secretary Jeremy Hunt said: 'It is extremely disappointing that junior doctors have voted against this contract, which was agreed with and endorsed by the leader of the BMA Junior Doctors’ Committee and supported by senior NHS leaders.
'The BMA’s figures show that only forty per cent of those eligible actually voted against this contract, and a third of BMA members didn’t vote at all. We will now consider the outcome.'