Sir Julian Hartley, chief executive of NHS Providers, which represents NHS trusts, warned that staff morale is low across the service and urged the government and the British Medical Association (BMA) to end the industrial action.
Junior doctors are in the middle of a six-day strike, which is the longest walkout in the history of the health service.
Figures published by NHS England on Friday show the number of flu patients in England jumped by more than a third over Christmas, with more than 1,000 people in hospital with the virus in the run-up to the strike.
Covid-19 patient numbers are also continuing to rise, though norovirus levels appear to have peaked.
The figures give a snapshot of pressures on hospitals in the week to December 31, a time when the NHS was finalising its plans for dealing with the strike.
An average of 1,312 people were in hospital each day last week with flu, including 81 in critical care beds.
The total is up over a third (39 per cent) from 942 the previous week, and more than double the 648 recorded a fortnight earlier.
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