Mr Hunt has not ruled out conciliation via Acas in future, but has rejected the move at this stage.
MPs shouted 'Where is he?' as the health secretary was not in the chamber to respond to Ms Alexander's question: 'To ask the secretary of state if he will make a statement on negotiations for new junior doctor contract?'
Responding on behalf of Mr Hunt, primary care minister Alistair Burt told the Commons that negotiations on the junior doctor contract had begun three years ago, based on the view - shared by government and the BMA - that the existing deal was outdated and in need of reform.
Junior doctor contract talks
'Extensive negotiations between 2012 and 2014 were 'abruptly terminated by the BMA’s unilateral withdrawal from negotiations without warning in October 2014', the minister said.
Both the secretary of state and NHS Employers had 'invited the BMA repeatedly to engage in negotiations', Mr Burt said, and had finally issued a contract offer at the start of this month.
He restated details of the offer, which would not increase overall funding for junior doctors and would leave some who work longer hours facing a reduction in pay, but would redistribute existing funding to allow an 11% increase in basic pay. Mr Burt said the offer had 'safety at its heart'.
Mr Burt told MPs: 'We deeply regret that the BMA chose the path of confrontation rather than negotiation.'
He told the Labour shadow health secretary: 'The honourable lady has called for the parties to go to Acas. The secretary of state is not ruling out conciliation. We have always been willing to talk - the government has repeatedly called for the BMA to return to the negotiating table and that offer is still open.
Junior doctor strikes
'We believe talks, not strikes, are best for patients and for junior doctors.'
Mr Burt said the health secretary had offered talks 'with no preconditions' apart from remaining within the existing pay envelope. But he added: The government reseveres the right to impose a contract if no progress is made on the issues preventing a truly seven-day NHS as promised in the manifesto and endorsed by the British people at the last election.'
But Ms Alexander hit back: 'The fact we are here today with 98% of junior docs having voted to take significant industrial action for the first time in 40 years makes me angry and sad. It didn’t have to be this way.'
With 'less posturing' from the health secretary, the current situation could have been avoided, she said.
On Mr Hunt's refusal to go to Acas now, she said: 'Does this flippant rejection not show casual disregard of patient safety? Does the minister understand that negotiation by press release is not the way to talk to junior docs and not the way to run the health service?'
After a letter from NHS England medical director Professor Bruce Keogh sought assurances that striking doctors would respond in an emergency, she said: 'There isn’t a single junior doctor who wouldn’t drop anything to respond to a major terrorist incident.
'Why is this government picking a fight with the very people who keep our NHS running?'
With just days to go until industrial action began, it was 'now time to talk' she warned.
Mr Burt insisted the government's door remained open and that it was 'for the BMA to come through' to get talks restarted.