The Prime Minister was left humiliated after almost 100 Conservative parliamentarians voted against plans to introduce so-called vaccine passports for larger venues in England. Some 96 Tory MPs voted down the measures, meaning they only went through with the support of Labour.
Earlier, Mr Johnson addressed the 1922 Committee of backbench Tory MPs, in a bid to decrease the size of the revolt - but the votes suggest this move was unsuccessful.
Sir Geoffrey Clifton-Brown, treasurer of the 1922 Committee, urged the Prime Minister to change his ways and consult MPs on Covid measures - and warned he could otherwise be “in danger” of a leadership challenge.
Sir Geoffrey said he was "very surprised" by the size of the rebellion, adding it "shows quite a major division within the party".
He told Sky News: "I think now the Prime Minister's really got to think very carefully about how he's going to reset his performance, to actually govern with a united party because we will know what happens to disunited parties."
On the prospect of Mr Johnson facing a leadership challenge in the New Year, Sir Geoffrey said: "I think that's got to be on the cards. He's got to realise that he's got to change."
Sir Charles Walker, the vice-chairman of the backbench 1922 Committee, described the rebellion against Covid passes as a "cry of pain" by the party and said Mr Johnson is in a “very, very difficult position”.
Former Tory chief whip and leading rebel, Mark Harper, said the Prime Minister has been sent a “clear message”.
He added: “This clearly isn't a good night for ministers or for the Government. You either listen and you respond and you do things differently or you ignore what you have been told and you plough on regardless and then this will happen over and over again.
"That choice is for the Prime Minister. I hope he makes the right choice, changes how the Government operates. We can do things better and I very much hope that we do."
Labour leader Sir Keir Starmer voted with the Government in all four votes on Tuesday evening but pilled further pressure on Mr Johnson.
Sir Keir said the result of the Covid pass vote was a "very significant blow to the already damaged authority of the Prime Minister".
He added: "I think it's very important to understand how deep the breach of trust is between the Prime Minister and his own party."
Shadow health secretary Wes Streeting has claimed Mr Johnson's authority is "shattered".
Mr Streeting added: “I think he has got to ask himself if he is the right man to lead our country through the next phase of the pandemic."
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