NICOLA Sturgeon has been criticised by the UK Statistics Authority for repeatedly claiming the prevalence of coronavirus in Scotland is five times lower than it is in England.
The regulator said the sources used to make the comparison do not "allow for a quantified and uncaveated comparison of the kind that was made".
The Scottish Conservatives accused the First Minister of using "dodgy statistics" for her own political purposes.
Party leader Jackson Carlaw said: "The issue here is that public confidence in government decisions should not be undermined by made up figures to substantiate political party spin."
He added: "People across the country take the First Minister at her word and now we know that they were repeatedly misled on this fact."
He called on Ms Sturgeon to apologise.
However, the First Minister said she stands by "the view, which I think is backed up by the evidence, that prevalence of the virus is significantly lower in Scotland right now than in England, although this is not something I have a shred of complacency about".
She said the issue with the comparison is that the "UK, English part of that statistic has not been published, and that is not down to me".
Miles Briggs, the Scottish Conservatives' health spokesman, had queried the statistical comparison with the UK Statistics Authority.
The regulator has now sent a critical letter to Roger Halliday, the Scottish Government's chief statistician.
Ed Humpherson, its director general for regulation, wrote: "When unpublished figures are quoted in the public domain, we expect that this information is shared with the media and the public in a way that promotes transparency and clarity.
"There are lessons to be learnt in this case, with different data sources being quoted to the media and to us.
"We expect that any figures used are appropriately sourced, explained and available in the public domain.
"Furthermore, it is important to recognise that a comparison of Covid-19 prevalence rates is not straightforward.
"If it is to be undertaken, the results and the uncertainties should be communicated transparently.
"We do not think that the sources above allow for a quantified and uncaveated comparison of the kind that was made.
"In future if such comparisons are made, we would expect to see sources made publicly available and a clear explanation of the limitations and associated uncertainty."
Mr Carlaw raised the issue during First Minister's Questions in Holyrood on Thursday.
He said it was said it was "unacceptable" for Ms Sturgeon to try to downplay it.
He said: "Ministers used it to explain the timing of lockdown being eased.
"When the Scottish tourism industry was crying out for a positive message, the First Minister refused to shut down the idea of closing the border, using that prevalence statistic as the basis.
"Nicola Sturgeon used this prevalence figure to suggest her policy was working better compared to elsewhere in the UK."
Ms Sturgeon accused the Scottish Conservative leader of a "bizarre" attempt to pretend Scotland has not made the progress it has.
She said: "I genuinely find myself right now feeling quite sorry for Jackson Carlaw.
"I have been a politician for 30 years and I still can't imagine getting so bound up in bitter, partisan politics that I can't bring myself to welcome the fact that we have made such progress against a deadly virus.
"How blinded must you be to find yourself in that position? My tolerance for this king of politics is lower than it has ever been before."
Mr Briggs said: “This verdict could not be more clear – the First Minister repeatedly gave a misleading picture of the state of the outbreak across the UK.
“This flawed analysis was the basis of major policy decisions and had serious repercussions for our tourism industry and our society.
“The First Minister’s use of these dodgy statistics even led to repeated warnings that the border could be closed which, in turn, triggered ugly protests that have damaged Scotland's reputation as a welcoming country.
“It is hard not to conclude that the First Minister pushed this unreliable comparison, with no context, for her own political purposes.
“The First Minister must apologise for misleading the Scottish Parliament and the Scottish public.”
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