Professor Stephen Powis told a Downing Street briefing there would also be increased testing of health staff in hotspot areas.
He said: “To protect our staff and our patients we will be introducing – with tests provided by the Test and Trace service – regular testing for staff in these high-risk areas, even when they don’t have symptoms.
“This will help us keep staff and patients in those hospitals as safe as possible.
“Secondly, we have asked the Nightingale hospitals in Manchester, Sunderland and Harrogate to prepare for this next phase.
“They are being asked to mobilise over the next few weeks to be ready to accept patients if necessary.
The Nightingale hospitals were set up during the peak of the pandemic across the country to help ease the burden on local health networks in case they ran out of beds.
They did not admit patients normally, only accepting people from hospitals that were struggling with space.
Seven were established in London, Birmingham, Bristol, Exeter, Harrogate, Manchester and Washington in the North East.
They ended up being barely used, with only London and Manchester admitting any patients and all of them were mothballed by July.
The government has defended the establishment of the Nightingale hospitals despite their use.
The news that they are being reopened is a worrying sign in the course of the pandemic.
England’s deputy chief medical officer, Professor Jonathan Van-Tam said there has been a steep rise in the number of people needing urgent treatment for coronavirus.
Hospital admissions are currently at around 600 a day, well below the peak back in May when there were more than 3,000 new daily admissions.
There are currently more people in hospital with coronavirus than there were when the nation went into lockdown in March
Professor Powis said there is still no cure or vaccine for Covid-19 and that more people are now in hospital with coronavirus than before restrictions were announced in March.
“Sadly, as the number of those infected increases, then so will the number of people who die,” he said.
“And that’s why the Government is looking at what other measures could be introduced in the areas where infection is rising the most.
“As the Secretary of State for Health has said, if we do not take measures to control the spread of the virus, the death toll will be too great to bear.”
He added: "In the over-65s - particularly the over-85s - we are seeing steep rises in the numbers of people being admitted to hospital so the claim that the elderly can somehow be fenced off from risk is wishful thinking."
Prime Minister Johnson is expected to announce a new tier system for imposing local lockdowns around England later today.It is understood Liverpool will be put under tier three while other northern areas currently under local lockdowns will avoid the harshest measures.