The comments were made in a call on Wednesday (23 July), The Times newspaper reports.
Meanwhile, while new NHS England boss Sir Jim Mackey said the service would be ‘much more resistant' to the demands of the BMA.
‘We and you make decisions about safety, not the BMA. Do what you do best, make sensible decisions and we'll stick together,' Sir Jim is reported to have said.
The comments come as NHS England has asked hospital chief executives to keep routine operations going to the fullest extent possible during this round of strikes by resident doctors and only reschedule appointments and other activity in exceptional circumstances to safeguard patient safety.
Thousands of resident doctors are expected to walk out from 7am on Friday 25 July until 7am on Wednesday 30 July.
The NHS is therefore advising the public to continue to attend any planned appointments they have scheduled over the strike period unless they have been contacted to reschedule.
The public should use 111 online as the first port of call for urgent but not life-threatening issues during industrial action so that they can be directed to the best place for their needs. Patients who need emergency medical care should continue to use 999 or come forward to A&E as normal.
Professor Meghana Pandit, NHS England national medical director, said: ‘There is no doubt this industrial action will take a toll on patients and NHS staff, and it is disappointing it is going ahead.
‘While it will mean some appointments won't be able to go ahead as planned, we are doing all we can to limit this, and patients should continue to use NHS services in the usual way.'