Professor Jason Leitch speaking at a Covid-19 briefing on Tuesday, was asked whether the current wave of the virus was the last for the public and scientists to worry about.
Responding, he said there would likely be a fourth wave, but it was unlikely to lead to another lockdown.
Prof Leitch said: “I don’t think this is the last time we need to be concerned about Covid.
"Most of the epidemiologists think there will be some kind of ‘winter wave’ along with flu and respiratory viruses, we just don’t know the scale of it.
"Vaccination appears to be really helping us now and we hope booster doses, protecting the vulnerable and continuing with some hygiene measures – and we’ll hear more about those baseline measures next week – will help us keep that to a minimum.
"But we will treat every wave at the moment we get in an appropriate way.
"I don’t expect to lockdown for wave four, but I expect we might have to adjust some things depending on what we find in the data and the advice we give the First Minister."
Prof Leitch was also asked about population immunity, whereby there is enough immunity in a population from a virus to restrict its ability to infect and transmit.
The national clinical director said most scientists estimate that somewhere between 70 and 80 per cent of all Scots would need some sort of immunity for population immunity to be achieved.
He said he believed Scotland was “beginning to turn that corner”, but warned population immunity was not a “magic moment where Covid will disappear”.
Prof Leitch said: "There is not a magic number. There is quite a lot of myth about population and herd immunity, it doesn’t suddenly happen that you meet 72.5 and the disease disappears. It is much more gradual.
"I am very hopeful that we are reaching those kind of levels now and that is why our numbers are falling because vaccination and pre-existing disease … is beginning to turn that corner.
"That is what we are seeing in Scotland and I think it is probably what we’re also seeing in England’s data over the last few days, later than our data."
The comments came as the First Minister indicated it was likely the planned relaxation of restrictions for August 9 would go ahead as planned.
Nicola Sturgeon said: “I am confident we will make progress and, while are already living with far fewer restrictions than has been the case in previous stages of the pandemic, all of us want to see the remaining restrictions eased as soon as possible.
“That’s important to all of us as individuals, it’s very important to businesses and the economy, but we will need to do that with appropriate caution and an appropriate degree of care.”
The First Minister said a “new milestone” had been reached as more than four million people have received their first dose of a Covid-19 vaccine and urged those who have not yet taken up their vaccine offer to do so.
Ms Sturgeon also strongly encouraged pregnant women to come forward to be vaccinated.