While Humza Yousaf conceded ministers had previously had concerns about such a measure, he added the recent spike in Covid-19 cases meant that “circumstances have changed”.
His comments came the day after First Minister Nicola Sturgeon announced that coronavirus vaccine certificates are being brought in as a condition of entry for nightclubs and other large events, such as music festivals and some football matches.
Ms Sturgeon announced the plans as she warned it is “by no means impossible” that Scotland could see 10,000 new infections of coronavirus a day.
Cases in Scotland are now five times higher than they were four weeks ago, with the First Minister stressing the situation was still “extremely concerning”.
To help combat the spread of the virus, the Scottish Government plans to bring in the vaccination certification scheme, which will apply to clubs as well as unseated indoor live events with more than 500 people in the audience.
The measure, which is due to be approved by Holyrood next week, will also be applied at unseated outdoor events with more than 4,000 in the audience, and at any event with more than 10,000 in attendance.
Nightclubs in Scotland only reopened for business on April 9 and the Scottish Licensed Trade Association (SLTA) has already branded the scheme a “most unwelcome development”.
SLTA managing director Colin Wilkinson said: “We are seeing a large spike in infection rates following the general reopening of the economy when a number of sectors fully reopened and Scottish schools have been opened for two weeks, universities and colleges are about to open, but nightclubs alone have been targeted with the possible introduction of a Covid status certification system at this time.”
However Mr Yousaf said the Government had opted to bring in the vaccine certification scheme instead of imposing wider restrictions.
The Health Secretary said: “Ultimately we are bringing this forward because we don’t want to reimpose restrictions, we never have wanted to introduce restrictions, no government wants to restrict people’s behaviours in any shape or way.
“But of course that is always an option we have to consider, particularly if we see the rise in cases we got last week.”
Mr Yousaf told BBC Radio Scotland’s Good Morning Scotland programme that while the sharp rise in cases last week had given ministers “significant concern”, the early indications from this week’s figures suggested “hopefully that the rate of increase is beginning to slow down”.
He added that while cases were not yet declining “the rate of increase is beginning to slow down”.
But with Covid infections 80% higher than a week ago, Mr Yousaf added: “We’re at a stage where we think Covid vaccination certification, the benefits of that could outweigh some of the risks.”
While he accepted there had been concerns, including around equality issues, Mr Yousaf said some “workarounds” had been created, so that for example those who do not have smartphones will not lose out.
Anyone who has had both doses of coronavirus vaccine can get a paper copy of the certificate to prove this.
Mr Yousaf also stressed the new vaccine certification scheme was being limited to “very, very specific events and very specific venues”.
He said: “That is a demonstration of the fact we still have concerns, but my central point is the benefits of a certification scheme, in terms of the public health intervention, in terms of incentivising vaccination, those benefits outweigh the concerns that still remain.”
While he said it would have been “premature” to have discussions with affected venues prior to the plans being announced to MSPs, Mr Yousaf said talks could now take place.
He added that nightclubs had “consistently” been regarded as “high-risk venues”, citing the lack of ventilation in venues and the “close contact” between clubbers.
Speaking about the new proposals, Mr Yousaf said: “I understand there is scepticism, but not only have circumstances changed, we have managed to find some workarounds around some of those issues.”