In a letter to the UK Statistics Authority, Scottish Labour’s Jackie Baillie labelled Mr Swinney’s comments “deeply concerning” and “erroneous”.
But a Scottish Government spokesperson dismissed Labour’s claims as “totally unfounded”, saying Mr Swinney’s comments referred not to the fresh restrictions brought in on boxing day, but to those already in effect such as the mandatory wearing of face coverings.
Mr Swinney told BBC Good Morning Scotland on Tuesday that figures from the Office for National Statistics (ONS) showed restrictions in Scotland were protecting the population, as infection rates were lower than in England.
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He cited an infection survey carried out in the week to December 23, before new restrictions on large gatherings and hospitality came into effect on December 26.
Ms Baillie said the use of these figures was selective, and risked “eroding public trust”.
A spokesperson for the Scottish Government said Mr Swinney was referring to restrictions previously in place.
"Prior to Boxing Day there were already substantial differences in Covid protections between Scotland and England – most importantly on wearing face coverings,” a spokesperson said.
“The Deputy First Minister made the entirely valid point that the different approach we are taking in Scotland is helping protect the population from the virus, using the latest available ONS data published at the time.”
Mr Swinney was asked on Tuesday if the Scottish Government was considering further measures in Scotland, despite Boris Johnson suggesting no such step would be taken in England.
He said: “I think there's a really important distinction in the data in Scotland with the data in England.
“That's demonstrated by the ONS infection study, which came out last week which demonstrated that whilst one in 40 individuals in Scotland are likely to have Covid just now, one in 25 are likely to have it in England.
“That to me is the strongest evidence that the measures we have taken in Scotland are protecting the population from Covid, but crucially also protecting our National Health Service from a greater scale of burden than the very high scale of burden that it is currently wrestling with.”