The measures are set to be reviewed every four weeks. However, pubs can remain open if they are serving "substantial meals".
The Liverpool City Region includes six local authorities – Halton, Knowsley, Liverpool, Sefton, St Helens and Wirral, which are all impacted by the closure.
In a statement to MPs in the House of Commons this afternoon (Monday 12 October), Johnson outlined the new alert system.
“[We are] introducing a three-tiered system of local Covid alert levels in England, set at medium, high and very high," he said.
"The medium alert level will cover most of the country and will consist of the current national measures. This includes the rule of six and the closure of hospitality at 10pm.
"The high alert level reflects the interventions in many local areas at the moment. This primarily aims to reduce household to household transmission by preventing all mixing between different households or support bubbles indoors.
"In these areas, the rule of six will continue to apply outdoors where it is harder for the virus to spread in public spaces as well as private gardens. Most areas which are already subject to local restrictions will automatically move into the high alert level."
Johnson highlighted a number of areas where these restrictions will apply and also laid out the measures for the strictest tier.
"As a result of rising infection rates, Nottinghamshire, east and west Cheshire and a small area of high peak will also move into the high alert level," he said.
"The very high alert level will apply where transmission rates are rising most rapidly and where the NHS could soon be under unbearable pressure without further restrictions.
"In these areas the Government will set a baseline of prohibiting social mixing indoors and in private gardens and closing pubs and bars.
"In each area we will work with local government leaders on the additional measures which should be taken.
"This could lead to further restrictions on the hospitality, leisure, entertainment or personal care sectors but retail schools and universities will remain open."
Sectors to close
The Prime Minister went on to say the Liverpool City Region will be placed into the sharp end of the new system later this week.
"We have been able to reach agreement with leaders in Merseyside," he added. "Local authorities in the Liverpool City Region will move into the very high alert level from Wednesday (14 October).
"In addition to the baseline I have outlined, as well as pubs and bars, gyms and leisure centres, betting shops, adult gaming centres and casinos will also close."
This follows a joint statement from Liverpool city leaders yesterday (Sunday 11 October), which stated the Government had decided to close on-trade venues in the area.
The Prime Minister is expected to give a televised address to the nation at a Downing Street press conference later this evening with Chancellor Rishi Sunak and chief medical officer Chris Whitty.
Following the PM's Commons statement, it was then revealed while pubs and bars will close, they can remain open where they operate as if they were a restaurant.
This means if they are serving "substantial" meals, like a main lunch or evening meal and can serve alcohol as part of this meal.