Professor Jason Leitch’s comments come as Cyprus became one of the first countries in the world to say it was seriously considering bringing in a vaccine passport system for British people travelling to the island.
Such a system would allow those who have received a vaccination to travel to certain countries provided they can prove they were vaccinated.
Other policies such as extending such a provision to the hospitality sector or the domestic tourism sector have been suggested by some within the UK.
Responding to questions on whether she believed vaccine passports would be coming to Scotland, Nicola Sturgeon said there were many “issues” around the proposal.
She said: “There’s some big unanswered questions yet about the impact of the vaccine on transmission and then there are all of the issues, if we’re going down that road, of how it works, how we avoid the inequities, how we make sure we don’t disadvantage certain groups and certain people.”
Prof Leitch said the introduction of vaccine passports would have “massive implications” in any country.
He said: “A vaccine to change behaviour to allow you to do more things, that has massive implications for your citizens across your country and therefore we need to think about that very, very carefully in the advice that will not just be public health advice, it will have to be much broader than that, on society, on ethics, on hospitality and tourism and everything else that would go along with it before that goes to decision makers for decisions.
"There are things we can do to be ready and we are starting to have those conversations about a digital solution to whether you’ve been vaccinated, whether you’ve been tested, whether you’ve been in contact with other people, and we can start to build the blocks for that as time passes.
"The big decision of what it will mean for Scotland and how we will engage with the rest of the world, we haven’t made those decisions yet.”
Asked whether young people could end up excluded from hospitality or from going on holiday due to being at the bottom of the list for vaccines, the First Minister said that situation was unlikely to arise.
Ms Sturgeon said: “We aim to have the whole adult population vaccinated by the end of July, so that includes young adults, people at the upper end of their teens, early 20s, so that proposition doesn’t really arise.
"I also worry about younger teenagers who have had their lives in the last year just completely turned on their heads, so getting them back to school, opening up the ability for them to have greater normality.”
Prof Leitch said once 4.5 million people have been vaccinated in Scotland, the population is protected, “even the unvaccinated”.
He said: “We have to be careful with a vaccination certification process. We have to be careful that we don’t exclude sections of the society by age, by social demographic, by whatever else, in allowing some people to do some stuff and other people not.”