Jason Leitch, speaking on BBC Good Morning Scotland, was responding to a question from club promoter Donald Macleod who had asked whether the scheme should be scrapped due to its failure to keep high risk venues open.
The certification scheme was brought in with the aim to make high capacity events and nightclubs safer, however both will be either see reduced capacity or closed altogether for three weeks after Christmas.
John Swinney announced nightclubs would be closed for three weeks at an appearance at Holyrood’s Covid-19 committee on Thursday.
Professor Leitch said he believed it would be “right” to look again at vaccine passports and indicated the advice would likely suggest a further roll-out of the scheme.
He said: "I think we need to review the Covid certification in light of the new variant.
"What Donald doesn’t have in his question there of course is that we brought in Covid certification and then we got a new variant.
"Let’s be clear, the virus did this, this isn’t because the timing of things in the restrictions was wrong. We got a new variant, the world got its fourth variant four weeks before Christmas.
"But I think he’s right that we need to look at Covid certification in light of the new variant.”
He added: "I think though the public health advice would actually be, probably, to expand it, to allow more places to open in light of the work around the new variant.
"Now Donald won’t like that, he’ll be yelling at the radio, but that would probably be the public health position.
"The final decision about that will be made by the First Minister of Wales for theirs, the First Minister of Scotland for ours etc., you can see countries moving and struggling with what that might look like.
"Most European countries, most mainstream European countries, now have a version of Covid certification to allow people to attend events and environments safely.”
Professor Leitch was also asked whether he believed the government was right to have allowed football games to go ahead last weekend despite Omicron.
He said: "I was comfortable last weekend with things happening, they were worrying me and I was on your programme talking about why they were worrying me and trying to get people to do them safely.
"I’m also comfortable with now what the SPFL have done and I am grateful to them to bring their winter break forward to allow that three week period where we won’t have that challenge, where people won’t be travelling, people won’t be in supporters’ buses, and the virus will have a chance not to spread in those environments.”