Ministers were warned that the disease in the South is following the hotspot pattern of the North, but just a few weeks behind.
The number of people being hospitalised and dying from the virus is also expected to be higher than previously thought.
The alarming warnings came from Steven Riley, professor of infectious disease dynamics, Imperial College London, which published the startling REACT report.
It put R - the rate of transmission - in London at close to three, though Prof Riley cautioned that these regional figures may not be accurate.
He stressed that lockdowns had “terrible implications” on people’s well-being and livelihoods.
But he also told Times Radio: “What the data was showing today would suggest, if that was going to happen, if the trade-offs are going to be worth it, and they very well might be, then we should think about timing....maybe sooner is better than later.
“The description of the patterns in different parts of the country are showing there would be real benefits.
“Even though the levels of infection are different around the country, we are showing a pattern in the southern regions that looks very much like the pattern in the northern regions a few weeks ago.
“The amount of virus, the prevalence is higher in the North, and then in the South and the Midlands we are seeing these faster growth rates.
“It’s clear that there would be substantial benefits across England for more stringent interventions, if they are justified.”
Ministers are still sticking to the three tier-system of localised interventions.
However, Professor Riley added: “Unfortunately it does show that the overall approach of trying to do the least possible in the smallest possible area...which is what lots of countries around the world are trying to do...that that is not working as well as we would hope.”
Asked what will happen if no further action is taken, he explained: “Clearly the number of infections is going up and the age distribution of those infections is not just in the young people, it’s clearly spreading out into the older ages who are more at risk.
“The inevitable conclusion of these findings is that hospitalisations and deaths are going to increase more quickly than we had thought until these data were seen.”
However, Communities Secretary Robert Jenrick told Sky News the Government was doing everything it could to avoid a full national lockdown.
It comes after France and Germany have announced second national lockdowns, of varying degree, to try to curb a surge in coronavirus cases and deaths.
Mr Jenrick said: “Of course we are informed by our scientific advisers, we are very grateful for them. But, as I say, they themselves would acknowledge that the role of government is to balance that out with the broader harms that come with a full long national lockdown.
“And we will do everything we can to avoid that. But obviously we will keep all of the options under review as you would expect us to.”
He insisted that the best approach was the localised model, adding: “Despite the fact the virus is rising across the country it is very concentrated in some places nonetheless.”
However, the scientists at Imperial College are warning that the second wave has reached a “critical stage”, with infections doubling approximately every nine days.
The Government said yesterday that a further 310 people had died within 28 days of testing positive for Covid-19. This brings the UK total to 45,675.
Separate figures published by the UK’s statistics agencies for deaths where Covid-19 has been mentioned on the death certificate, together with additional data on deaths that have occurred in recent days, show there have now been 61,000 deaths involving Covid-19 in the UK.
The Government said that, as of 9am on Wednesday, there had been a further 24,701 lab-confirmed cases of coronavirus in the UK. It brings the total number of cases in the UK to 942,275.
The Imperial researchers said they are detecting early signs areas that previously had low rates of infection are following trends observed in the country’s worst-affected regions.
They added that there has to be change before Christmas, and if more stringent measures are to be implemented, it needs to be sooner rather than later as the current measures are “not sufficient”.
The interim data from round six of the React study uses data and swab results from 86,000 people between October 16-25, and estimates there are around 96,000 new infections per day.
According to the study, the overall prevalence of infection in the community in England was 1.28% - or 128 people per 10,000, up from 60 per 10,000 in the previous round which took place between September 18 and October 5.
Infections were doubling every nine days with a national reproduction number (R) estimated at 1.56, compared to 1.16 in the previous round, according to the Imperial College London study.
The report suggests interim estimates of R were above 2.0 in the South East, East of England, London and South West, but there is a greater degree of uncertainty around these figures.
The experts warn: “The co-occurrence of high prevalence and rapid growth means that the second wave of the epidemic in England has now reached a critical stage.
“Whether via regional or national measures, it is now time-critical to control the virus and turn R below one if further hospital admissions and deaths from Covid-19 are to be avoided.”
They add that the pandemic is growing exponentially, but say the effect of some of the most recent measures may not have filtered through to the numbers.
The experts found the prevalence of infection was highest in Yorkshire and The Humber at 2.72 per cent, up from 0.84 per cent.
In the North West it was at 2.27 per cent, up from 1.21% per cent, and lowest in the East of England at 0.55 per cent, up from 0.29 per cent.
According to the study, prevalence increased across all age groups with the greatest rise in those aged 55-64 at 1.20 per cent, up from 0.37 per cent.
The data suggests the clustering of Covid-19 cases was more prevalent in Lancashire, Manchester, Liverpool and West Yorkshire, West Midlands and East Midlands.
Professor Paul Elliott, director of the programme at Imperial from the School of Public Health, said: “I think we were disappointed to see that actually we were still in this rapid growth phase - except, as we say, in the North East where there does seem to have been a turn down, but it’s still growing.”
He added: “It’s more critical, because it’s gone up more and it’s continuing to go up.
“And also we’re seeing this increase in the rate of rise, rather than decrease in the rate of rise which we did spot before.
“So there was a period when the rate of rise was decreasing, and we were hopeful that the policies that have been implemented were turning the rates down and ultimately turning the prevalence down.
“But what we see this time is an increase in the rate of rise and not only a high prevalence in the north, increasing rapidly increasing prevalence in the south.”
The React study was commissioned by DHSC and carried out by a world-class team of scientists, clinicians and researchers at Imperial College London, Imperial College Healthcare NHS Trust and Ipsos Mori.
The data is released as a pre-print and has not been peer-reviewed.