Health Secretary Jeremy Hunt has confirmed that the government will push through the current version of the working contract for junior doctors, despite objections and without further negotiation.
In a statement to parliament, he said a phased introduction of the new contract would go ahead as planned from October, to end the "impasse" between the two sides which risks further damaging the NHS.
In May the government and NHS Employers reached a "historic agreement" with the British Medical Association on a new contract for junior doctors after more than three years of negotiation and "damaging strike action".
The deal was backed by leader of the BMA's Junior Doctors Committee, Dr Johann Malawana, and was supported publicly by the vast majority of Medical Royal Colleges. However, junior doctors rejected the terms on offer, with 58 percent of the 68 percent turnout voting against the contract.
"Because of the vote we are now left in a no-man's land that," Hunt said, adding: "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 the patients who depend on it".
Dr Malawana, who resigned from his position on the result, said the vote was a "demonstration of just how appallingly frontline staff have been treated and undermined".
"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".
"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," he stressed.