The controversial new contract for junior doctors in England will begin to be rolled out from today.
The new deal for training medics sparked the biggest walk out of doctors in the history of the NHS.
From today, some obstetrics and gynaecology trainees will transition to the new terms and conditions of service.
The British Medical Association (BMA) described it as a "watershed moment for the NHS".
The union's junior doctor committee chairwoman Dr Ellen McCourt said that the Government was "ploughing ahead" with the new deal "ignoring the outstanding areas of concern raised by junior doctors".
The BMA has written to all NHS trust chief executives across the country requesting that they pause the introduction of the new contract if certain conditions are not in place.
The letter states that trusts are not compelled to use the new deal and reminds them that certain requirements must be in place before they can legally introduce it.
The BMA has also provided training medics a letter template so they can write to their bosses and press them to delay the introduction of the contract until all the requirements are met.
It has also provided an email template for juniors to notify their HR directors that they are "working under protest" if they do not wish to accept the 2016 terms and conditions of service.
Dr Ellen McCourt, BMA junior doctor committee chair, said: "Today is a watershed moment for the NHS, as some junior doctors will be moved on to a contract which they have rejected. It couldn't come at a worse time, as a recent BMA study found that almost half of junior doctors are looking to move overseas, given their morale is at an all-time low.
"As the Government ploughs ahead with the contract, ignoring the outstanding areas of concern raised by junior doctors, many hospitals trusts may feel they have little choice but to rush to implement the new terms and conditions.
"A great deal of preparation is required for the new contract to be put in place, but very little time has been allowed for this, due to the Government's politically imposed deadline.
"We know that a number of trusts have decided not to start using the contract in October and the BMA is calling on all trusts to hold off the introduction of the contract if any of the required arrangements are not in place.
"Introducing a new contract requires major systemic change and will affect a generation of junior doctors. It is vital for the time to be taken to get it right, rather than rushed, for no other reason than to meet a political timeline."
Since January, junior doctors have staged a series of strikes protesting against the new contract, which is being brought in for all doctors below consultant level.
The BMA had also planned a series of five-day strikes in the run-up to Christmas but called them off due to patient safety fears.
The new deal will be rolled out from today, initially to obstetrics and gynaecology trainees going into their fifth year of training, with other junior doctors transitioning to the new conditions throughout the rest of 2016 until October 2017.
Last week, NHS Improvement said it had been supporting trusts across the country to prepare to introduce the contract, with many junior medics getting involved in the contract implementation.
Yesterday, Neena Modi, professor of neonatal medicine and president of the Royal College of Paediatrics and Child Health, said the staffing contract is "damaged goods".
In an editorial published in The British Medical Journal, Prof Modi said the document should be "discarded and replaced with one drawn on a clean sheet".
Last week, the campaign group Justice for Health - founded by five junior doctors - lost a High Court challenge against the Secretary of State over the new deal.
Justice for Health said that Jeremy Hunt had acted beyond the scope of his powers by compelling NHS employers to adopt the contract. But Mr Justice Green dismissed the claim.
The judge concluded that Mr Hunt had approved the contract, but had not compelled employers to adopt it.
A Department of Health spokesman said: "Following last week's judicial review ruling, we must now move on from this dispute to the crucial job of making sure patients get the same high standards of urgent and emergency care every day of the week, which involves more than the junior doctors' contract."