Travellers from Cyprus and Lithuania will have to self-isolate on arrival in Scotland for 14 days.
The measures will be introduced on Sunday due to a “significant rise” in cases of coronavirus in the countries and the associated risk of importation.
It comes as UK Transport Secretary Grant Shapps announced similar restrictions in England.
Justice Secretary Humza Yousaf said: “It is evident both in Scotland and in countries across the world that the virus continues to pose real risks to health and to life, and we need to interrupt the rise in cases.
“Imposing quarantine requirements on those arriving in the UK is our first defence in managing the risk of imported cases from communities with high risks of transmission.
“That is why we have made the decision to remove Cyprus and Lithuania from the country exemptions list.
“Whether or not an overseas destination has been designated for quarantine restrictions, our message remains clear that people should think very hard before committing to non-essential foreign travel.”
The measures will come into effect at 4am on Sunday.
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