Mr Johnson told Sky News : “There are between ten and 30 places where you are seeing it bubbling up a little bit.
“I think the country as a whole understands that the best way to deal with this is if we have tough local lockdowns to get it under control in those towns.”
After praising Leicester’s “huge effort” in reacting to the first local lockdown in Britain, Mr Johnson warned the country cannot get complacent, adding it would be wrong to assume “somehow we’re out of the woods.”
“It is absolutely vital that as a country we continue to keep our focus and our discipline and that we don’t delude ourselves that somehow we’re out of the woods or that this is all over, because it isn’t all over,” he added.
But Mr Johnson defended the way the government has handled the country’s response to the pandemic, which has seen nearly 46,000 lives lost from the virus.
Speaking on a visit to North Yorkshire, he said there has been “a massive success now in reducing the numbers of those tragic deaths”.
It comes after the PM warned a second wave of the virus could hit within two weeks.
A Downing Street source told the Mail: “The PM is extremely concerned by what he’s seeing abroad and fears we could be seeing the same thing here in a fortnight.
“People have got to realise we are still in the middle of a pandemic.
“He wants to go further on opening things up and getting people back to work, but he knows it’ll be his head on the block if things go wrong.”
Worrying data shows the number of new Covid-19 infections has risen sharply as ministers fret over fears of a second spike.
Towns including Oldham, Rochdale, Blackburn with Darwen and Luton have been battling spikes, as has the city of Bradford.
Scientists at Cambridge University have said it is “very likely” that most regions in England are close to the point at which the virus begins to spread exponentially.
The data from the Cambridge MRC Biostatistics Unit found that four out of seven English regions have seen a rise in infections in recent weeks.
The south-east and the south-west now have an R rate above 1, meaning the infection is spreading in these areas.
Top 10 places where cases have grown in the last two weeks
Hyndburn : From 6 to 54 – growth rate of 9
Eden : From 4 to 33 – growth rate of 8.25
Sandwell : From 40 to 163 – growth rate of 4.08
Hackney : From 30 to 90 – growth rate of 3
Trafford : From 33 to 99 – growth rate of 3
Swindon : From 23 to 56 – growth rate of 2.43
Birmingham : From 130 to 295 – growth rate of 2.27
Blackburn with Darwen : From 107 to 242 – growth rate of 2.26
Barnet : From 23 to 49 – growth rate of 2.13
Walsall : From 28 to 58 – growth rate of 2.07