The Labour leader asked how members of the public are supposed to understand the rules when Boris Johnson does not understand them himself.
It comes after Mr Johnson had to apologise after muddling his words when asked to explain new rules on social gatherings.
He made the mistake only a few hours after his minister Gillian Keegan was unable to say whether households in the north east of England could mix in pub gardens under new regulations.
Sir Keir told the Commons: “One of the major problems, as we’ve seen in the last 24 hours, is widespread confusion about the local restrictions and I don’t just mean the Prime Minister not knowing his own rules – having sat opposite the Prime Minister at PMQs every week that didn’t come as a surprise to me.
“Let me quote to him the Conservative council leader in Bolton, a Conservative leader. He said this about the Government’s handling of restrictions: ‘it’s breeding resentment, it’s become too complex, too complicated, people feel very let down and very frustrated and very forgotten’.
“If the Prime Minister doesn’t understand the rules and his own council leaders are complaining about mixed messages, how does the Prime Minister expect the rest of the country to understand and follow the rules?”
Mr Johnson replied: “Actually, I think that the people of this country do understand and overwhelmingly do follow the rules, and that I may say is in spite of the efforts of [Sir Keir] continually to try to snipe from the sidelines, to undermine what we are trying to do, and he mentions the restrictions in the North East, and I cleared that matter up as fast as I could.”
The Prime Minister used PMQs to swipe at Labour’s shadow education secretary who suggested the pandemic could be a “good crisis” for her party.
Mr Johnson said: “One day they’re theoretically marching side by side with the rest of us trying to defeat coronavirus, the next minute they’re off in the undergrowth firing from the sidelines.
“It was the shadow education secretary [Kate Green] who really revealed what Labour is all about, she said this was a good crisis which they intended to exploit – we see this as a moment for the nation to come together.”