A spokesman for the First Minister said people across the UK would be "deeply embarrassed" by the Prime Minister's remarks at the Conservative Party conference on Sunday.
Environmental groups also criticised Mr Johnson, describing the move as "petty", and are calling for Scottish ministers to make its own plans for a series of events outside the summit in 2020.
The UN climate change conference, which is being co-hosted by the UK and Italy, is expected to be the most important gathering on the issue since the Paris agreement was signed in 2015.
The summit at the Scottish Events Campus in Glasgow will be the largest the UK has ever held, with around 30,000 delegates and up to 200 world leaders attending.
Put a flag on it
During a Scottish reception at the Tory conference in Manchester, Mr Johnson said he wanted to "put a Union flag" on every Government policy to hammer home the benefits of the UK.
Giving the UN summit as an example, he added: "The leaders of the entire world will come to Glasgow and I don't mind seeing a Saltire or two on that summit, but I want to see the Union flag.
"I don't want to see Nicola Sturgeon anywhere near it, because the Scottish nationalist party didn't secure that summit in Glasgow, it was the United Kingdom Government."
A spokesman for Ms Sturgeon hit back on Monday, saying that voters would be "deeply embarrassed to hear their Prime Minister acting so childishly".
He added: "It is right that the COP26 conference should come to Scotland given our leadership in climate action.
"We were one of the first countries in the world to acknowledge the global climate emergency and the Scottish Government has introduced the toughest targets in the UK to ensure our action matches the scale of our climate ambitions.
"When it comes to issues of common concern such as climate change, the SNP government are proud to play our part and work in partnership with other governments – something that Boris Johnson seems completely incapable of doing."
Left Out Again?
Dr Richard Dixon, director of Friends of the Earth Scotland, said it was “inevitable" that the UK Government would try to freeze Scotland out of the conference.
"The only surprise is how honest the Prime Minister has been about Scotland’s exclusion and about how petty the UK Government is prepared to be," he added.
Scotland's energy minister Paul Wheelhouse also attacked Mr Johnson over his remarks, writing on Twitter: "He is a bully and like all bullies, he is a coward and can’t stand a strong woman or anyone else standing up to him."
Scottish Greens co-leader Patrick Harvie said the Scottish Government "must have a formal role" in the UN summit as it was taking place in Scotland.
“To reduce this important global summit about how we respond to the biggest crisis facing our future to a shallow flag-waving exercise only reveals why Boris Johnson should not be anywhere near the position of Prime Minister," he added.
This story originally appeared on inews.co.uk