SNP leader Nicola Sturgeon criticised the Prime Minister after he told Conservative MPs on Monday that devolution had been "Tony Blair's biggest mistake".
Douglas Ross, who leads the Conservatives in Scotland, insisted that "devolution has not been a disaster" in response to Mr Johnson's remarks on Monday.
Downing Street sources did not deny Mr Johnson made the comments, which were first reported by the Sun, during a discussion with the Northern Research Group of backbenchers.
Mr Johnson called the MPs from Number 10, where he is self isolating after coming into contact with an MP who later tested positive for coronavirus.
It came as he tried to "reset" his leadership after a turbulent year from coronavirus, and Downing Street in-fighting.
In response to the comments, which included Mr Johnson saying he could not "see a case" for handing down more powers, Scotland's First Minister suggested independence was the best answer for the devolved administration.
Ms Sturgeon tweeted: "Worth bookmarking these PM comments for the next time Tories say they're not a threat to the powers of the Scottish Parliament - or, even more incredibly, that they support devolving more powers.
"The only way to protect & strengthen ScotParl is with independence."
Mr Ross countered the Prime Minister's comments, which come just a few months before the Scottish Parliament elections next year.
The Moray MP, who plans to stand in the vote to become an MSP in May, said: "Devolution has not been a disaster.
"The SNP's non-stop obsession with another referendum - above jobs, schools and everything else - has been a disaster."
Only last month the UK's three devolved administrations raised concerns over the Westminster Government's UK Internal Market Bill, with the Scottish Government describing the legislation as a "power grab".
The Prime Minister called the MPs who represent constituencies in northern England as he tries to unite the party after facing sustained criticism throughout the pandemic, and bitter in-fighting inside Downing Street culminated in the departure of his chief aide, Dominic Cummings.
Asked about his comments on devolution, a No 10 source said: "The PM has always supported devolution but Tony Blair failed to foresee the rise of separatists in Scotland.
"And leaving the EU means we must strengthen and protect the UK economy with the UK Internal Market Bill.
"Devolution is great - but not when it's used by separatists and nationalists to break up the UK."
The House of Lords Select Committee on the constitution warned the Bill could "destabilise" devolution, with peers suggesting ministers listen to the concerns and amend it - or scrap the relevant powers entirely.
Analysis of a study examining public opinion at the beginning of November also suggested the pursuit of Brexit is undermining support for Scotland remaining in the UK.