The country was added to the register of quarantine-free destinations less than two weeks ago.
Quarantine has been reinstated for travel from Denmark after a series of outbreaks in the country.
Now, arrivals into Scotland must self-isolate to "safeguard public health."
Travellers arriving in Scotland from Denmark must quarantine for 14 days - and must self-isolate at home or another address from 12.30pm today.
The decision to remove Denmark from the quarantine exemption list is being taken on the basis of public health advice following discussions on Thursday evening between all four Chief Medical Officers in the UK about reported cases in humans of a variant strain of the coronavirus associated with outbreaks in mink farms in Denmark.
It comes after other UK nations made similar decisions.
Justice Secretary Humza Yousaf said: “The virus continues to pose significant challenges in Scotland and around the world and we are taking this immediate step based on clinical advice, to help further safeguard public health and keep communities safe.
"This also underlines our consistent message that people should think very hard before committing to non-essential foreign travel.”
Scotland’s Chief Medical Officer Dr Gregor Smith said: “The Chief Medical Officers met last night and we have recommended this immediate action on a precautionary basis.
"I am liaising with the other UK CMOs today to consider updated information and assess whether we should advise Ministers to take any further steps beyond quarantine.”
“The Chief Medical Officers are clear that action is required to safeguard public health.
“If anyone has any concerns, as in any case, whether or not they have travelled from Denmark, they should follow the guidance laid out by Scottish Government and if needed, contact NHS 24.”
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