Managers will have to ensure that doctors who volunteer to work more than 48 hours a week during any resurgence of the flu pandemic have it “agreed in writing”.

Department of Health director of workforce capacity, values and equality Flora Goldhill has written to senior managers with an update on the European working time directive. Ms Goldhill said the letter was intended “to clarify key points around some of the questions arising for their [junior doctors’] reassurance”.

She said an “opt out” of the 48 hour week, or 52 hours in a derogated rota, must be agreed in writing and would be needed to support the NHS through the swine flu pandemic or to provide extra cover for a short term vacancy. Any extra clinical activity carried out under an opt-out is still covered by trust indemnity, she added.

The letter also said that junior doctors’ hours were referenced over six months, and therefore there was “no strict rule” about the hours worked in a week under the directive as “hours are averaged over six months”.

Ms Goldhill wrote: “We should all ensure our junior doctors are supported, informed and understand their position regarding indemnities, that it is in their interests to check they accurately record the hours they work, and that opting out is wholly voluntary.”