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The experts said an immediate "circuit breaker" was the best way to control cases, at a meeting on 21 September.
Communities Secretary Robert Jenrick insisted the government had taken "robust action" that "balanced" the impact on the economy.
But Labour has described the documents as "alarming".Â
It comes as the Liverpool region prepares to enter a "very high" Covid alert level from Wednesday, the highest of a new three-tier system.
Most areas of England will be on "medium" alert, with measures such as the rule of six, but areas with local restrictions on household mixing are automatically on "high" alert.
A "very high" alert sees pubs and bars close if they do not serve "substantial meals", almost all household contacts banned and advice against travel.
Speaking at a press conference on Monday evening, Boris Johnson said the alert system for England could succeed in driving cases down if it was implemented "very effectively", and he rejected the "extreme route" of a full nationwide lockdown "right now".
But at the same briefing, England's chief medical officer, Prof Chris Whitty, voiced concerns over the impact of the new rules, saying he was not confident the "base measures" in the highest tier "would be enough to get on top of" the virus.Â
"That is why there's a lot of flexibility for local authorities [...] to do significantly more," he said.
Released shortly after the announcement, minutes from the meeting of the Scientific Advisory Group for Emergencies (Sage) - which feeds into UK government decision making - stated the advisers had called for the immediate introduction of a short national lockdown three weeks ago.
The papers also showed the scientists suggested:
- banning all contact inside homes with members of other households
- closing all bars, restaurants, cafes, indoor gyms and hairdressersÂ
- requiring all university and college teaching to take place onlineÂ
Of all the measures proposed by the advisory group, just one - advising those who can work from home to do so - was implemented by the government at the time.
In the documents, Sage warned that "not acting now to reduce cases will result in a very large epidemic with catastrophic consequences".Â
Speaking to BBC Breakfast, Mr Jenrick said the government had introduced measures such as the rule of six at the time, and stressed the Sage papers had contributed to the measures the PM announced on Monday.Â
He said they had taken "balanced judgements" that weighed up the effect on the economy and "all the other unintended consequences" of measures, such as the impact on mental health and delayed surgeries.Â
On the new three-tiered system, he said: "We are now able to have a very clear and consistent framework across the whole country, so people will be able to understand approximately what the rate of infections is in their own area and what the rules are accordingly."
He later told BBC Radio 4's Today programme that the baseline measures for the highest tier "will have an impact", and ruled out any other areas joining the Liverpool City Region in the highest tier this week.
But he said plans for other parts of the nation would be "kept under review".
Labour's shadow health secretary Jonathan Ashworth told BBC Breakfast he was "alarmed" by the Sage papers, adding: "Ministers need to tell us why they've rejected that advice to go further."
He also insisted the government was going to have to go further than the latest measures.Â
"As we head into the winter things are getting really serious now," he said.
Cases are increasing across the whole of the country and the number of people in hospital is now higher than before the full lockdown in March. We are at a critical stage in the epidemic.
It is at this moment the gulf between the official scientific advice and the decisions made by government has been laid bare.
It is the case that "advisers advise and ministers decide". When considering new measures to stop Covid, government must also take into account the harms they cause to our health and the economy.
But there is some concern the government is doing too little, too late.Â
And that we can either choose the terms for controlling the virus now, or wait and the virus will force our hand as it did with lockdown in March.