Prof Ferguson is the scientist whose modelling convinced the prime minister to impose the first lockdown on 23 March last year.
In June last year, he told MPs deaths during the first wave could have been halved if Johnson had started that lockdown one week earlier.
And speaking on The Guardian’s Today in Focus podcast on Monday, Prof Ferguson suggested Johnson – and other European leaders – didn’t “learn” that “acting earlier saves lives”.
Watch: 'Politicians only act when they see people in hospital' expert says
After a summer in which COVID-19 infections were minimised, cases started to increase in the autumn and Johnson admitted on 18 September that the UK was in the second wave of the pandemic.
It took Johnson until 5 November to impose a second national lockdown on England, having been urged to take action at numerous points in October.
While the second wave was accelerated by an unforeseen element – the more transmissible variant identified in Kent in the winter – Prof Ferguson said: “I think it was very unfortunate that the lessons from the first wave – namely that acting earlier saves lives and doesn’t actually have a higher economic cost than acting later – that lesson wasn’t learned.”
He went on: “Unfortunately governments across Europe only really acted once they saw exponentially increasing numbers of cases and [hospitalisations] rather than believing the data from their test and trace systems.”
While Prof Ferguson said he was “encouraged” by the decision to effectively lock down over Christmas – when festive mixing was banned apart from on Christmas Day in most of the country – he suggested schools should have been shut during the second national lockdown, between 5 November and 2 December.
“The closure of schools is the big difference between the third lockdown and second lockdown. Our modelling showed the second lockdown was not sufficient to control this new variant – you needed to have schools shut to control it.”
Watch: 2020 footage of Neil Ferguson talking about COVID
On Monday, meanwhile, Johnson warned that the third wave currently seen in Europe will "wash up on our shores".
He told reporters in Preston: “People in this country should be under no illusions that previous experience has taught us that when a wave hits our friends, it washes up on our shores as well.
“I expect that we will feel those effects in due course."
However, the UK will this time have the advantage of having rolled out one of the world's most successful vaccine programmes, with 27,997,976 people having received a first dose as of Sunday.
Nonetheless, England's chief medical officer Prof Chris Whitty has previously warned the next COVID wave will still cause "significant numbers" of deaths later this year, partly because the vaccines are not 100% effective and partly because some people will choose not to, or are unable to, get a jab.
Watch: How England is leaving lockdown