The Prime Minister is believed to have been urged by some ministers not to use 1980s public health laws to respond to the pandemic as it meant Scotland and Wales had control over how they responded to the crisis.
Mr Johnson was said to have instead been urged to use the 2004 Civil Contingencies Act, which gives Whitehall supreme authority for a “catastrophic emergency”.
According to The Sun, the matter was raised repeatedly at both Cobra and Cabinet, with Commons leader Jacob Rees-Mogg particularly supportive of using the sweeping Act rather than writing a new one.
A former aide who has now left government said: “At the time I think everyone just assumed there would be a joined-up response across the whole country and we didn’t really think at the time it would splinter.
"But obviously that turned out to be wrong and was pretty naive.”
A Cabinet Minister added: “I have no doubt that it will be done differently next time. The PM knows that."
Mr Johnson’s spokesman on Tuesday refused to deny the reports.
He said: “As we have done throughout the pandemic, we have worked closely with the devolved administrations as we’ve moved through various phases of the pandemic.
“As the Prime Minister said, we work best when we are together.”
The SNP’s shadow Cabinet Office minister Stewart Hosie MP has now accused Mr Johnson of trying to bypass Holyrood.
He said: "While the First Minister's priority is to lead Scotland through this devastating pandemic and to put public health first, it's shameful that Boris Johnson and his Tory Cabinet colleagues have instead talked up overruling the powers of the Scottish Parliament and undermining devolution once again.
"People in Scotland have made clear that the leadership they want through the pandemic and which they trust is that of Nicola Sturgeon – not Boris Johnson.
"The issue at the election in May will be this; who has the right to decide what sort of country Scotland should be after the pandemic – people in Scotland or Boris Johnson? With both votes SNP on May 6, we can put Scotland's recovery in Scotland's hands – not Boris Johnson's.”