Professor Jason Leitch told the BBC that young teens could be vaccinated in "the near future", pending advice from the UK's four chief medical officers.
His comments come after the news that the UK’s vaccine advisory body has refused to green-light the move to vaccinate teenagers between 12 and 15 years-old.
The Joint Committee on Vaccination and Immunisation (JCVI) said it would widen the vaccine roll out to more children who have underlying health conditions.
Speaking to BBC Radio Scotland’s Drivetime, Prof Leitch said: “They haven't come down and said do or don't do it - they said we're not recommending it yet - we're going to keep looking.
"The health ministers have written to CMOs and said could you give us advice in the round - not just about the individual risk per kid, but also look at the educational environment, the time off school, the safety of schools.”
He added: "There absolutely could be a decision to roll out vaccination for 12 to 15-year-old’s. The final decision will be with ministers and I would have thought that would be a four-country decision."
Humza Yousaf, Scotland’s health secretary said that Dr Gregor Smith, the country’s chief medical officer, has been asked to explore “as soon as possible” whether there is additional evidence supporting the vaccination of young teenagers.
He said: "A further update will be issued once these discussions have taken place.
"In the meantime, we will offer the vaccine to those children and young people currently recommended."