Health secretary Humza Yousaf admitted he has “ethical, clinical and human rights concerns” about the domestic use of vaccine passports.
Mr Yousaf also revealed the Scottish Government has yet to make a decision on their use in Scotland.
It comes after Scottish Liberal Democrat leader Willie Rennie asked the government for an update on the controversial issue.
What is a vaccine passport?
Currently, Scottish ministers are working on a potential digital system which the public could use to show they have received both doses of a coronavirus vaccine.
A vaccine report card is being issued in England, but it is not being offered in Scotland.
The absence of a confirmed plan on this issue already led to Scottish GPs being inundated with requests for a form of proof of their vaccination earlier this month, in case one day it becomes essential for ordinary activities such as staying in a hotel, going to a public event or buying a plane ticket.
Some GP surgeries have appealed to patients not to ask for proof of vaccination because they do not have the capacity to provide these, but official NHS guidance says patients have a right to access their medical history.
“No decision” has been taken on domestic use of vaccine passports
In parliament on Wednesday, Mr Yousaf said: “As a Covid status programme progresses, it will be replaced by a digital Covid certificate, and that is likely to include vaccination status Covid recovery and negative testing data.
“For international travel we are working with common travel areas to put in place a digital solution that aligns with international standards.
“No decision has been taken on using them domestically, but I do have ethical, clinical and human rights concerns about their use.
“I am about to host a round table on human rights to discuss this.
“I want to give assurance – no decision has been made about using these certificates for domestic use.”
The new health secretary, appointed to the role by Nicola Sturgeon last week, also said this would be a way of making sure GPs are not inundated with requests for their patients.
He added: “These certificates have a low currency value as not many countries require them, and no major airline requires them.
“This is to stop inundating GPs who are working extraordinarily hard.
“We are not pressing ahead with vaccine certificates until we resolve these issues and have cross-party discussions.”
Mr Rennie had raised concerns about the wider policy after earlier security flaws were detected.
The Lib Dem leader said: “There is no clarity on how these will work, what they will be used for and for how long. It seems like the government is making it up as it goes along.”
Scottish Government looking at online registration for vaccines for all under 50s
Meanwhile, the health secretary also confirmed the Scottish Government is looking into using online registration for coronavirus vaccinations for everyone under the age of 50.
This comes after online registration for a coronavirus vaccine for those between the ages of 18 and 29 opened up earlier this week.
It comes after half of people who were due to receive their coronavirus vaccine over the weekend failed to turn up.
Mr Yousaf said: “I am talking to them team about using the online portal for 18 to 29 year olds and extending that to 30 to 39 year olds and 40 to 49 year olds.
“That is urgently being looked at, and those who didn’t attend their vaccine appointment are being followed up.
“We are exhausting every avenue and will do everything we can.”