This follows the front cover of The Independent today (pictured above) accusing Whitehall officials of having "sexed up" the case against a strike called by the British Medical Association.
The letter was written by Sir Bruce Keogh, the medical director of the independent body NHS England, and approved by Health Secretary Jeremy Hunt.
It was made public in November, a week after the Paris attacks, and caused uproar among junior doctors, with three thousand medics then writing to Keogh accusing him of using fears of a terror attack for "political purposes".
Revisions of the letter, seen by The Independent, had been made to ensure concerns about the possible impact of a major incident during the strike were made as "hard-edged" as possible, the paper reports, with another headline suggesting the Government "put words in the mouth" of Hunt.
A Department of Health spokesperson said: "Industrial action of the kind planned by the BMA creates a major safety risk for patients so it was absolutely right that ministers insisted on Sir Bruce Keogh giving his independent view of the NHS' capacity to respond in the event of a major terrorist incident — particularly in the days following the devastating attacks on Paris.
"Given it is the Government's ultimate responsibility to do everything it can to ensure public safety, it is completely right that the department expressed a view on communication with the BMA."
Junior doctor strikes due to start next week were called in opposition to Hunt's proposed new working conditions. Many have argued that the strike is a matter for the British Medical Association and Hunt, and that Keogh should not have got involved.