Professor Jason Leitch says he is still worried about the "overwhelmed nature" of the health service as the legal requirement to wear face coverings comes to an end in Scotland.
The national clinical director said coronavirus is now being dealt with through common sense and guidance rather than law.
He spoke to the BBC's Good Morning Scotland radio programme on Monday, saying it was the first time he had been in the studio in person in two years.
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Vaccination and therapeutics have "changed the game", Prof Leitch said, but he acknowledged the daily case rate was still high.
He said: "We're still cautious as public health advisers because we're still worried about the overwhelmed nature of our health systems around the world - not just here, but Scotland is no exception.
"Our emergency departments are struggling, our hospitals are struggling, not just with Covid - with backlog, with everything else coming in that has waited until this point to come forward."
During the pandemic many people have been waiting before approaching the health service with their illness.
Prof Leitch was asked about the fact he had not been convinced by the effectiveness of face coverings early in the pandemic.
He said he wished he had known at that stage about the extent of asymptomatic transmission and the airborne nature of the virus.
The national clinical director was also asked about a video showing Nicola Sturgeon not wearing a face mask during a campaign visit to a barber's at the weekend.
He said: "I haven't spoken to the First Minister today, I imagine I'll speak to her later.
"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 is if you are in a crowded area inadvertently or deliberately, then put a face covering on and that will protect you and others."
Scottish Conservative MSP Craig Hoy said it was inappropriate for a civil servant to defend the First Minister's actions.
He said: "These kinds of questions should be left to politicians to answer. Instead, SNP ministers are in hiding and Jason Leitch is blurring the lines between ministers and government officials.
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"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."
