Professor Jason Leitch has defended Nicola Sturgeon after she was filmed without a face mask in a hairdresser for "a matter of seconds" over the weekend.
The First Minister has been reported to Police Scotland after a clip online showed her without a covering while in a barber shop on Saturday in East Kilbride.
Police confirmed they had received a complaint and said it was being assessed.
The SNP said Sturgeon was invited into the barbers during an outdoor visit on the street.
On the BBC 's Good Morning Scotland show National Clinical Director Professor Jason Leitch said the FM forgot to wear a covering for a short moment, saying it happened to him recently.
He added: "I've got up from the dinner table quite recently out for a meal gone to the bathroom and halfway there you realise 'oh, I need to put my face covering on' because because this does still feel like a slightly odd thing to have to do.
"My understanding is it was a matter of seconds, she realises the place is crowded, puts her face covering on which is actually what we're asking people to do.
"The guidance says if you are in a crowded area, inadvertently or deliberately, then put a face covering on and that will protect you and others."
An SNP spokesman said: "Within a few seconds, she realised she hadn't put her mask back on and immediately put it on."
A Police Scotland spokesman said: "We can confirm that we have received a complaint which is currently being assessed."
People are no longer legally required to wear face masks on public transport and in most indoor public spaces in Scotland as the rule moved into guidance from today.
However although the final coronavirus restriction in law has lifted, the Scottish Government is still strongly recommending that people continue to wear face coverings where appropriate as Covid-19 continues to spread.
Craig Hoy, Scottish Conservative MSP, said it was "inappropriate" for Leitch to be defending the First Minister.
He added: "It is inappropriate for a civil servant to defend Nicola Sturgeon in this way. These kinds of questions should be left to politicians to answer. Instead, SNP ministers are in hiding and Jason Leith is blurring the lines between ministers and government officials.
"Mr Leitch is also misrepresenting the Covid laws as they stood when Nicola Sturgeon clearly broke them at the weekend.
"Face mask use was still in law until today but Mr Leitch backed up Nicola Sturgeon's excuse that she only had to put the mask on when in a crowded space.
"If the SNP had listened to us weeks ago and changed face mask rules from law to guidance, he and Nicola Sturgeon would have been correct.
"But they failed to do this and Mr Leitch should not be confusing the public, or doing the SNP's job for them, by trying to defend Nicola Sturgeon in this manner."
Prof Leitch was asked about the state of the virus in Scotland on GMS.
He said: "We have to keep in the back cupboard anything we can. There's no way you can rule anything out in the middle of this.
"The WHO (World Health Organisation) has a committee that decides the kind of escalation level for the world.
"It meets every so often to decide if the pandemic is over.
"So the question the question is, is the pandemic over? And it met last week and it said, no, definitively, no, this pandemic is not over.
"Most experts think it's halfway through globally. So we're probably two years or four or five before we can take our foot off the accelerator entirely."
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