Prof Peter Horby said the UK was at a "precarious point" as Covid-19 cases and hospital admissions continue to rise.
It comes after England's deputy chief medical officer warned the country was at a "tipping point".
Ministers say their local approach to restrictions is the right way forward.
The prime minister is expected to announce tougher local restrictions on Monday.
In a statement to MPs, Boris Johnson will outline plans for a three-tier system, where each region in England is placed into a tier based on the severity of cases in the area.
Later on Sunday, he will hold a call with cabinet ministers to update them on the next steps.
Across the UK, the R number - the average number of people each infected person passes the virus on to - is now estimated between 1.2 and 1.5.
Anything above 1.0 means cases are increasing.
On Saturday, 15,166 people in the UK were reported to have tested positive for coronavirus - up 1,302 on Friday's figure, according to the latest figures on the
government's dashboard. There were a further 81 deaths - a decrease of six on Friday.
'Difficult choices'
Prof Horby, chair of the New and Emerging Respiratory Virus Threats Advisory Group (Nervtag) and a government adviser, said the "critical mission" now was to protect the NHS to avoid non-essential hospital services being cancelled, as many were when the UK went into its first nationwide lockdown in March.
"We really need to provide care to everybody - those with Covid and those without," he said. "The way to do that is to keep the numbers down."
He warned that some hospitals in the north of England were already coming under pressure and it might not be long before intensive care beds fill up.
"I am afraid we are going to have to make some very difficult choices and act very quickly," he added.
Prof Horby said a surge in cases in the North was partly because people were coming into contact with more people than in other parts of the country.
He also told the BBC's Andrew Marr Show that in the months before the increase in cases, numbers had not dropped to as low a level in the North as in other parts of England.
Prof Horby said the country must accept more stringent measures to drive down transmission of the virus.
In an earlier statement, England's deputy chief medical officer
Prof Jonathan Van-Tam said the seasons were "against us" and the country was running into a "headwind" ahead of the winter months.
He warned more deaths would follow a rise in cases over coming weeks and urged people to limit social contact.
It is expected that parts of the north of England and the Midlands will be placed under tougher measures as part of the prime minister's announcement.
Liverpool, where there are currently 600 cases per 100,000 people, is expected to be placed under the most severe set of restrictions, with all the city's pubs forced to close.
Pubs and restaurants across the central belt of Scotland
closed their doors for at least two weeks on Friday, to try to tackle a rise in cases.