Travellers arriving in Scotland from Portugal will have to self-isolate for 14 days under new rules coming into force on Saturday.
Scotland and Wales have added the country to their “quarantine list” – while England and Northern Ireland have not.
UK Transport Secretary Grant Shapps said it was a confusing position but the Scottish government insisted it was acting on scientific advice.
The new rules are effective from 04:00
French Polynesia is also now on Scotland’s list of countries requiring quarantine, while self-isolation rules for Greece have been operating in since Thursday.
Justice Secretary Humza Yousaf said the decision to add Portugal came after coronavirus cases there rose above 20 per 100,000 of the population.
Mr Yousaf said: “We are in the midst of a global pandemic and the situation in many countries can change suddenly.
“Therefore, people should think very hard before committing to non-essential travel abroad.
“With Scotland’s relatively low infection rate, importation of new cases is a significant risk to public health.”
The Scottish government was also closely monitoring the situation in Gibraltar, he added.
But the move was questioned by UK Transport Secretary Grant Shapps who told the BBC’s Today programme the Scottish government had decided to “jump the gun” earlier in the week by adding Greece to its quarantine list without using data from the Joint Biosecurity Centre (JBC).
On Portugal, he said the decision had failed to take into account the increased level of testing. He said the positivity rate – the proportion of positive tests – was lower than it was when Portugal was added to the travel corridor list.
A spokesman for the Scottish government, however, said Mr Shapps made his decision to keep Portugal on travel corridor list before studying the latest JBC data.
Travellers returning to Scotland will be required to self-isolate even if they have flown back to an airport in England.
Prime Minister Boris Johnson later downplayed the difference between UK nations when questioned during a visit to the West Midlands.
While conceding the devolved administrations sometimes have different approaches, he insisted the UK was “proceeding as one”.
“I think you will find if you dig below the surface of some of the surface differentiations you will find overwhelmingly the UK takes the same approach,” he said.