The Bolton West MP described the new three-tier measures as “worse than the disease” in his resignation letter to Mr Johnson.
He said the latest plan had “failed” and was doing “damage to physical and mental health”.
Mr Green tweeted his resignation letter to the Prime Minister, writing alongside it: “The Bolton lockdown has clearly not worked, and I believe that the cure is worse than the disease.
“So I have stepped down from my role as Parliamentary Private Secretary.”
In a letter to the Prime Minister, Mr Green also criticised the coronavirus restrictions in his constituency of Bolton West and Atherton – saying the “attempted cure is worse than the disease”.
He wrote: “There is a healthy debate on how we can eliminate this coronavirus or how we can live with it and this is being led by many distinguished academics, epidemiologists and other specialists.
“I believe that there are better alternatives to the Government’s approach, so I therefore tender my resignation.”
MPs are expected to back the new three-tier lockdown system when they vote on restrictions in the House of Commons later on Tuesday.
This would mean the restrictions could come into force the following day.
But the Prime Minister has faced a backlash elsewhere from other Tories over the Government’s new plan.
Senior Conservative Sir Bernard Jenkin said local advice in his Harwich and North Essex constituency is a “short, sharp, shock” would be the best way of tackling the spiralling pandemic.
The chairman of the Commons’ powerful Liaison Committee told Times Radio: “If we nipped it hard now, we would be well back to manageable levels before Christmas.
“If we leave it for another five or six weeks, then the tail of the bell curve goes well into January.”
Earlier on Tuesday, Downing Street warned regional leaders who refuse to enter the highest level of the Prime Minister’s new restrictions that the Government does in fact have the power to “impoase” the measures regardless.
Liverpool City Region has so far only agreed to sign up to the Tier 3 restrictions, which bans households mixing indoors and the closure of pubs unless they can operate as resturants.
Mr Johnson’s spokesman was tight-lipped on which areas acxross the north of England, as well as Yorkshire and Humber, the government still wants to accept the severest restrictions.
But he added: “The Government does have the ability to impose measures if it’s considered that’s what’s needed to reduce transmission, to safeguard the NHS and to save lives.”
This is a breaking story. More to follow…