In a new guidance for junior doctors ahead of the strike scheduled for next week, the General Medical Council (GMC) said that in order to avoid patient harm "the right option may be not to take action that results in the withdrawal of services".
The rolling action - the first of its kind in the history of the NHS - will see junior medics withdraw labour, including emergency care, for a week each month until the end of the year.
But the GMC said the scale of the action at such short notice cannot be justified.
When will the strikes go ahead?
Junior doctors will go on strike between 8am and 5pm on:
September 12 to 16
October 5, 6, 7, 10 and 11
November 14 to 18
December 5 to 9
The Government and British Medical Association (BMA) remain at loggerheads over the contract, which the Department for Health says will provide a seven-day NHS.
The GMC guidance states: "Given the scale and repeated nature of what is proposed, we believe that, despite everyone's best efforts, patients will suffer.
"In light of this, the right option may be not to take action that results in the withdrawal of services for patients."
It is a doctor's responsibility to "put their patients first and protect them from harm", GMC chief executive Niall Dickson said.
Professor Terence Stephenson, chairman of the GMC, said:
I am extremely concerned about the impact which this prolonged campaign of industrial action will have on patients' care and on the public's trust in doctors.
Timeline of Junior Doctors' contract dispute
Six strikes have already taken place across England during the lengthy dispute, causing disruption to hundreds of thousands of patients
In May it looked as though a breakthrough had been reached in the dispute after both sides agreed to a new deal
Then in July, the Government announced that it would impose a new contract after junior doctors and medical students voted to reject the contract brokered between health leaders and the BMA
The BMA said it will call off the strikes if the Government agrees to stop the imposition
A BMA spokesman said: "Patient safety remains doctors' priority and since the announcement last week of further action, the BMA has been liaising with NHS leaders so that plans can be put in place swiftly to minimise disruption for patients.
"This action is still avoidable. The BMA has said it will call off next week's action if the Government puts a halt to plans to force junior doctors to work under a contract they have rejected because they don't believe it is good for the future of patient care or the profession."