Sir John Bell told MP's we shouldn't rely on the development of a successful coronavirus vaccine.
Sir John Bell said too many assumptions had already been made during the course of the Covid-19 pandemic.
Instead, he said, it would be advisable to prepare for the colder weather, and flu season, without depending on a breakthrough from researchers working on a vaccine.
His comments came in response to Greg Clark, chairman of the Science and Technology Select Committee, who asked if the country should be preparing for the winter without a vaccine, or if one might be ready in time.
Sir John said: "This whole epidemic has relied too heavily on assumptions that have turned out not to be true.
"So, my strong advice is be prepared for the worst."
The MPs also heard that it could be chaos in hospitals if the UK sees a resurgence of coronavirus this winter, alongside a serious flu season.
Sir John said it was therefore important to make sure that people were getting the flu vaccine.
He explained: "I think one of the things that clinical staff in hospitals worry about is if we do have a significant flu season.
"Then we are going to have a bit of a clinical problem if we've also got Covid running alongside because you'll get people with severe pneumonias arriving with fever and all the usual things, and it'll be pandemonium in the A&E departments.
"So, what I'm rather hoping is that first of all we ideally expand the number of people getting flu vaccines so we get better coverage, and secondly we push quite hard to make sure people are compliant and participate in the flu vaccine programmes.
"The uptake is lamentably small in some countries and I think we're not messing around anymore.
"This could be really serious if people don't get their vaccines."
Kate Bingham, chairwoman of the UK's Vaccine Taskforce, told the committee that while she was optimistic that a vaccine would be developed, in the short-term it may just be one that reduces the severity of the disease, rather than prevents people from getting it.
Asked when a vaccine may be available, she said maybe by early next year depending on the success of clinical trials.
Sarah Gilbert, professor of vaccinology at the University of Oxford, is leading the vaccine trial being run by researchers there.
She told the committee she hoped their vaccine might be ready earlier, but it depended on trials showing efficacy, and she could not put a time