Mr Johnson unveiled the new three-tier system in the Commons, with areas classed with a risk level of either medium, high, or very high risk.
The majority of the country has remained at a medium risk level, meaning restrictions stay the same.
But many northern areas, including South and West Yorkshire, have been re-categorised as high risk, meaning a ban on mixing households indoors from tomorrow.
However, in a Downing Street press conference tonight, Mr Johnson said he would like to see more agreements with local leaders in areas such as Yorkshire similar to that reached with Liverpool City Region mayor Steve Rotheram, whose area is one of few under the top tier of alert with bans on travelling and the closure of pubs.
Mr Johnson said the Government was still speaking to leaders in Yorkshire, suggesting the alert levels announced yesterday could yet change, and when asked if more areas would be in the very high risk category if local leaders had agreed, he said: “It’s absolutely correct to say we are working with local authorities [...] trying to work with them to support a collective package of measures.
“I was very pleased that Steve Rotheram of the Liverpool City Region came forward with a package, and the offer is that to all local leaders who are facing problems [and] big increases in the infection rates. we’ll help to support more local test and trace, more local enforcement, and so on.”
But he also appeared to suggest local areas could be overridden as he added: “Clearly we also have as a national government to think about our primary duty which is to save life and to protect the NHS, and we will also do whatever we think is necessary over the next few days and weeks.”
Mr Rotheram said on Twitter tonight he had not agreed to the measures, which were “dictated to us by Government”, but discussions had been over extra money and resources that would support the restrictions.
As it stands, North Yorkshire and Hull and the East Riding remained in the medium category, meaning the current national restrictions of the rule of six and 10pm curfew for hospitality venues continued.
Meanwhile Chief Medical Officer Professor Chris Whitty warned that even those with the strictest conditions may not quell the spread.
He said: “I am not confident - and nor is anyone confident - that the tier three proposals at their baseline would be enough.”
He added: “We’re going to have to do more [...] and probably in some areas significantly more.”
While Prof Whitty praised leaders in Bradford and said: “Bradford actually has shown superb leadership in the way that they have tackled this, if they had not done so [...] we would be in a substantially worse place than we are at the moment.”
However Sheffield City Region mayor and Barnsley Central MP Dan Jarvis: “Local leaders face a situation where we are left without the tools and resources to control the virus, until cases spiral to the ‘very high’ alert level. This is not the right approach.”
Mr Jarvis said that because being in the high category did not mean businesses such as pubs would have to close, Government support was not being offered.
But he said that the trade, and those that rely on it, would still be hit due to low demand as households are unable to mix.
Mark and Sona Young own Sela Bar in Leeds and said businesses in city centres had already been decimated by the 10pm curfew and people working from home.
The couple said they would feel more secure had Leeds been placed into tier, despite having a small handful of staff to pay.
Mrs Young said: “Businesses are lucky if they are taking 50 per cent of what they were taking this time last year.
“We’re in a position where, financially, we would be better off to be closed than in the tier we’re in here in Leeds.”
Former Leeds MP Greg Mulholland, from the Campaign for Pubs, said: “Pubs already are saying they wished they were in tier three, because they simply can’t stay open with these restrictions. Yet there is no support available for them.”
The Chancellor Rishi Sunak tonight said businesses not forced to close could access the Job Support Scheme for help.
But the TUC is urging MPs to demand answers from the Government on support for workers when the new measures are debated in Parliament tomorrow.
And Leeds City Council leader Judith Blake said: “None of us wants to see restrictions on life in Leeds, but we are deeply concerned that if cases continue to rise as they have been, this could not only mean further restrictions for the city, but it would also risk putting our local health services under increased and unsustainable pressure.”
Revealing the new system, which aims to simplify the patchwork of rules that had been emerging across the country, Mr Johnson told the Commons: “The weeks and months ahead will continue to be difficult and will test the mettle of this country.”
He added: “This is not how we want to live our lives, but this is the narrow path we have to tread between the social and economic trauma of a full lockdown and the massive human and indeed economic cost of an uncontained epidemic.”
He later said: “The figures are flashing at us like dashboard warnings in a passenger jet and we must act now.”
He added: “No one affected by this will be left to fend for themselves.”
He said: “The number of cases has gone up four times in four weeks and it is once again spreading among the elderly and vulnerable.
“There are already more Covid patients in UK hospitals today than there were on March 23 when the whole country went into lockdown and deaths, alas, are also rising once again.”
And he said: “No one, least of all me, wants to impose these kinds of erosions of our personal liberty, but I am as convinced as I have ever been that the British people have the resolve to beat this virus and that, together, we will do just that.”
But Labour leader Sir Keir Starmer said he was “sceptical” whether the Government has a plan to get control of the virus.
Earlier Mr Johnson resisted calls from Yorkshire MPs to allow smaller areas to be lifted out of coronavirus restrictions rather than applying “arbitrary” rules to large parts of the country.
Shipley MP Philip Davies said there had been a “a constant blizzard of arbitrary rules which will only serve to collapse the economy and destroy businesses and jobs”, and the Conservative urged the PM to “put his trust in the British people to act responsibly” and apply “common sense”.
And Wakefield's Conservative MP Imran Ahmad Khan added: "The Conservative Party is the champion of individuals’ rights to make autonomous decisions without state interference. Will the Prime Minister double down on our party’s historic commitment to invest greater trust in the individual to decide what is best for themselves?"
But Mr Johnson replied: "Indeed, and I hope that the individual will also recognise that the risk that we carry—he or she carries—is not just to ourselves, but to the whole of the community because, in the end, we are all potential vectors of this disease and we may bring it inadvertently to someone who is more vulnerable than ourselves. That is the risk."
While Labour’s Tracy Brabin, MP for Batley and Spen, and Conservative MP for Colne Valley Jason McCartney also asked whether restrictions would be more granular if the data suggested some smaller areas could be removed from the rules.
But Mr Johnson said it was not possible and that “you have to keep your geographical areas fairly coherent”, despite varying infection rates across areas.
"I know that that causes a great deal of frustration for (MPs) and I have been hearing it for weeks and months, but that is the way that we have to do it," he said.
It was an answer also given to Thirsk and Malton’s Tory MP Kevin Hollinrake, who questioned how North Yorkshire - England’s largest county - could all be treated the same.
Earlier in the day Professor Jonathan Van-Tam, England’s deputy chief medical officer, said the second wave of coronavirus infections has emerged most prominently in the North because rates had not dropped as low as in the South at the end of the national lockdown.
Prof Van-Tam addressing a question about a presentation slide depicting a creeping rate rise in the South, said: “The epidemic this time has clearly picked up pace in the North of England earlier than it did in the first wave, and that almost certainly relates to the fact the disease levels in the North, and certainly in the North West, never dropped as far in the summer as they did in the South.”
But he said: “This is a nationwide phenomenon now that rates are changing upwards across the UK.”
Northern leaders have for weeks been claiming that the UK Government lifted the national spring lockdown restrictions with London and the South East in mind.
MPs in the North of England criticised the Government’s briefings on the new coronavirus restrictions as a “shambles” after some said they were invited to calls for the wrong region or even left off the list entirely.
Sheffield Heeley’s Louise Haigh said: “I got my invite 5 minutes after the meeting had started.”
While Hull West and Hessle’s Emma Hardy told the PM in the Commons a failure to contact all Yorkshire MPs and council leaders had created “confusion and fear”.
Mr Johnson said: “The Government at all levels has been in constant contact with authorities in Yorkshire for the last few days and I’m very grateful for their co-operation.”
While Normanton, Pontefract and Castleford MP Yvette Cooper called on the Prime Minister to “come back from the moon and get back to what’s happening on planet Earth” as she raised concerns over testing.
She said: “Just a month ago, the PM described his Moonshot plan where there were going to be millions of tests done and returned every day and he said if everything comes together, it may be possible even for sectors like theatres to have life much closer to normal before Christmas.
“Families now are feeling like a normal Christmas is going to be further away (than) ever and local health officials in our area have said people are waiting six days, not a day, to get their test results. If we come back from the moon and get back to what’s happening on planet Earth, when will he have enough testing capacity in place so my constituents can get their results in 24 hours?”
Mr Johnson replied: “The daily test process has gone up just in the last month by 34 per cent and daily capacity has gone up 28 per cent and as she knows, by the end of this month, NHS Test and Trace are confident they will be doing 500,000 tests a day, they will have capacity I should say for 500,000 tests a day.”
While Conservative Miriam Cates, MP for Penistone and Stocksbridge, asked about the arrangements for informal childcare under the new measures, telling the Commons: “As a new parent himself, I’m sure (Mr Johnson) understands that sometimes circumstances dictate that parents need emergency childcare and that’s happening more and more with childminders having to isolate, nursery staff etc.
“So can he confirm emergency informal childcare will still be able to assist parents even under the three-tier system?”
Mr Johnson replied: “Well, you know, tell me about it, Mr Speaker.
“I think she makes a very, very important point and the provisions we have for 30 hours’ free childcare are there. The point about emergency childcare is well made.”
Some 11 further deaths were recorded in Yorkshire today in people who had previously tested positive for coronavirus, bringing the region’s total to at least 3,021.
Nationally, 50 further deaths were reported, bringing the total to 42,875.