In a rare intervention by the chief officer of the House of Commons, Lindsay Hoyle scolded Johnson ahead of his weekly question-and-answer session for making rules in a "totally unsatisfactory" way.
Johnson is grappling with a swiftly spreading second wave of the coronavirus outbreak and growing anger over restrictions imposed on citizens.
"The way in which the government has exercised its powers to make secondary legislation during this crisis has been totally unsatisfactory," Hoyle told parliament.
Opposition leader Keir Starmer criticized Johnson's virus measures, saying that "people feel very let down, very frustrated and very forgotten."
Britain, which has the worst official death toll in Europe, reported 7,143 new cases of coronavirus on Tuesday, the highest single figure to date.