The two sides will attempt to resolve outstanding differences, which include Saturday pay and unsocial hours.
The government has put on hold, for five days, its plans to impose the contract.
The British Medical Association (BMA) has suspended its threat of further industrial action while the talks last.
This latest round of talks will be mediated once again by conciliation service Acas.
Ministers drew up plans to change the contract in 2012, but talks broke down in 2014.
Under the terms of the new contract, basic pay is to be increased by 13.5% on average, but other elements of the pay package are to be curbed, including what constitutes unsociable hours.
Day hours on a Saturday will be paid at a normal rate, while extra premiums that are being offered for the rest of the weekend are lower than what is currently paid.
As a result of the dispute between the government and the BMA, there were four strikes by junior doctors in England affecting routine - but not urgent care - between January and early April.
Last week, there were two one-day strikes affecting all forms of care, including emergencies - the first such action in the history of the NHS.
Meanwhile, researchers from Oxford University have said earlier findings backing the government's push for a seven-day NHS in England are based on flawed data.
One of the government's key arguments behind the push for a seven-day NHS in England - and a new contract for junior doctors - has been patient safety.
The new Oxford University paper concludes that hospital data suggesting a "weekend effect", where death rates are higher for those admitted over the weekend period, are deeply flawed.
It focuses on the Oxford Vascular Study covering more than 90,000 people in Oxfordshire, looking at hospital admissions for stroke between 2002 and 2014.
The researchers found more than a third recorded as being admitted for stroke were actually in for other things - often low-risk, routine procedures carried out on Monday to Friday.
They say these coding errors distorted the mortality figures, making them appear better for patients admitted on weekdays.
Without the mistakes, they argue, there was no "weekend effect".
They warn these errors are commonplace across the UK and not just for data on strokes.
The lead author, Professor Peter Rothwell, said it was time for an independent review to assess the "weekend effect".
"There's a wealth of poor-quality evidence based on hospital administrative data," he said.
"If you look at those studies that have actually done the due diligence and looked at real data - gold standard data - there's very little evidence indeed of a weekend effect.
"It really is an excellent example of how poor quality data, badly interpreted, can lead to the wrong answer."
He said government ministers had acted in good faith but had been "badly misled" by their advisers.
"Looking at where we are now, you could only describe it as a shambles," he said.
"We need to step back and work out to begin with is there a problem here that needs solving. The high-quality data suggests there's no problem to be solved."
BMA leader Dr Mark Porter said ministers should have been more careful.
"Yet again, this raises questions about the government's repeated use of misleading figures to undermine doctors and justify its pledge to increase seven-day services in the NHS," he said.
But Professor Nicholas Freemantle, from University College London, who co-authored an influential study in the British Medical Journal last year that highlighted a weekend effect, rejected the criticisms.
"He [Prof Rothwell] is raising issues we're very aware of and have done our best to take into account," he said.
"There have been enormous efforts to improve the data set in the period he's covered, so things have moved on.
"The statistical model we used was set up to use different aspects of the data sets. This model identifies patients likely to die with an extremely high degree of precision."
NHS England said: "This report about data collection covering one condition from nine GP practices in no way alters the wider issue that sick patients rightly should expect to be seen by a consultant within a few hours, have prompt access to tests and treatments and receive joined-up care, whatever day of the week they fall ill, as recommended by the Academy of Medical Royal Colleges."
Fresh talks aimed at ending the dispute over a new contract for junior doctors in England will get under way later.