Dr Susan Hopkins, PHE’s strategic response director for coronavirus, said the UK needed to “better prepared” than it was last autumn.
The spread of a more transmissible variant in the UK led to a surge of infections and prompted another lockdown over the winter.
Dr Hopkins told the BBC's The Andrew Marr Show: "I think we have to prepare for a hard winter, not only with coronavirus, but we've had a year of almost no respiratory viruses of any other type.
“And that means, potentially the population immunity to that is less.
"So we could see surges in flu. We could see surges in other respiratory viruses and other respiratory pathogens.”
She continued: "It's really important that we're prepared from the NHS point of view, from public health and contact tracing, that we have everything ready to prepare for a difficult autumn.
"We hope that it won't occur and it will be a normal winter for all of us."
Health Secretary Matt Hancock told a Downing Street briefing on Friday that deaths from coronavirus have fallen by 41 per cent in the course of a week, while hospital admissions have seen their fastest ever fall.
He said all the data showed “we’re heading in the right direction” and the vaccination programme “is protecting the NHS, saving lives right across the country”.
Dr Hopkins said she believed “we will all have our summer holidays” but her role as a Government advisor is to “prepare for worst case scenarios”.
"It doesn't mean that they'll necessarily happen, but my job is to make sure that we have options available for the country in case things are not as satisfactory as we'd all like them to be," she said.
Dr Hopkins said it was "highly unlikely" that a new Covid-19 variant would derail the plan to start easing England's lockdown "for the next three to five weeks".
But she stressed it was crucial that the situation was carefully monitored.
"We'll need to be very ready for an autumn that could be challenging as these variants are there,” she said.
"We're working very closely with vaccine manufacturers to see what they could do to develop new vaccines.
"But we're also very conscious of the fact that what happened last summer, in late summer and early September, could happen again and we need to prepare for that and hope that it doesn't happen."
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