In an unusually outspoken move, the organisation has rebuked the Prime Minister for “political posturing” and a “baseless mischaracterisation” of lawyers, which it said was “damaging to the rule of law”.
Mr Johnson, who has previously dismissed human rights lawyers also as “lefty”, said on Wednesday that "left-wing criminal justice lawyers act against the public interest".
Speaking on LBC radio, Mr Johnson was asked to respond to comments by Labour party leader, Sir Keir Starmer, that the Conservatives had become the party of crime and disorder.
He said: “When you look at Labour, you see a party that voted consistently against tougher sentences for serious sexual violent offenders. The Labour opposition has consistently taken the side of, I’m afraid, left-wing criminal justice lawyers against, I believe, the interests of the public.”
His comments came nearly a year after he told the Conservative Party conference the criminal justice system was being hamstrung by “lefty human rights lawyers”.
In a statement on its website, the Faculty of Advocates, which regulates the training and professional practice, conduct and discipline of advocates in Scotland, said it “deplores” Mr Johnson’s comments.
The body said: “These comments go hand-in-hand with recent pronouncements by the home secretary and appear to be part of a strategy to undermine the rule of law.
“It is essential to a fair system of justice that those charged with crime have legal representation. Without such representation, no conviction would be safe.
"For the Prime Minister to undermine that principle, with the aim of political posturing, is damaging to the rule of law.
“Lawyers represent their clients without associating themselves with the merits, or the politics, of their client’s position. They do so because that is their duty.
"The nature of this duty does not change, whether the lawyer is prosecuting or defending a case. The Prime Minister knows this and yet sees fit to make political capital from a baseless mischaracterisation. In so doing, he risks damaging the system of criminal justice irreparably.
“Moreover, the current rhetoric around lawyers is irresponsible and risks serious consequences.
"Those in the criminal justice system – judges, prosecution and defence – have kept the legal system afloat in very difficult circumstances. For the Prime Minister and his government to treat key workers in this manner is entirely unsatisfactory.”
Last year more than 800 former judges and legal professionals signed a letter accusing Mr Johnson and home secretary Priti Patel of "hostility" towards lawyers representing migrants seeking asylum.
Ms Patel had referred to "do-gooders" and "lefty lawyers" in a speech on what she called the "broken" asylum system.
Signatories to the letter claimed the Prime Minister and home secretary had “endangered" lawyers' safety with their comments.
At the time, a No.10 spokesperson said that, while lawyers played an important role in upholding the law, “they are, however, not immune from criticism”.