But Downing Street did not deny the comments.
He also said he saw no case for giving Scotland's semi-autonomous government and parliament, which are dominated by the pro-independence Scottish National Party (SNP), any further powers in addition to the ones they hold now.
"Devolution has not been a disaster", he said on Twitter.
'The only way to protect and strengthen the Scottish Parliament is with independence'.
"The SNP's non-stop obsession with another referendum - above jobs, schools and everything else - has been a disaster".
However, polls suggest that Scots have a more favourable view of how Sturgeon and her administration have handled the pandemic than the rest of the country has of how Johnson's government has performed.
The Prime Minister made the controversial comments in a Zoom call with MPs for northern England.
Downing Street issued a clarification just hours after reports of the initial comments surfaced: "The Prime Minister has always supported devolution but Tony Blair failed to foresee the rise of separatists in Scotland".
"The time has come for a more federal United Kingdom where we take more power out of Westminster, put it closer to people, and I think that in the long run will strengthen the country and build a better way of doing politics". But it said he was not criticizing devolution, only its use "by separatists and nationalists to break up the U.K".
Shadow Scottish secretary Ian Murray criticised Mr Johnson's remarks as he defended devolution as "one of Labour's proudest achievements".
Shadow Scotland Secretary Ian Murray declared: "This confirms that Boris Johnson doesn't believe in devolution and would put the future of the United Kingdom at risk".
"If they want to demonstrate that they are prepared to relent, and respect the will of the people in the devolved nations, they should immediately overhaul the Internal Market bill, with its assault on devolution, and finally commit to working with, not working around, the Welsh Government when it comes to the Shared Prosperity Fund and future funding for Wales". Instead, people across the United Kingdom have been paying the price for his failings.
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. The Prime Minister's disdain only serves to underline the growing threat we face.
Douglas Ross has been making a splash since he took over the leadership of the Scottish Tory party by being unafraid to disagree with Mr Johnson on Scottish matters.
The SNP would like voters to believe that the Conservative government in Westminster neither cares nor understands the needs and desires of people in Scotland.