UK Transport Secretary Grant Shapps has claimed Scotland “jumped the gun” by adding Greece to the quarantine list.
On Wednesday, the Scottish government moved Greece to the list of countries from where returning travellers have to self isolate for 14 days.
The Scottish government said its decisions on quarantine measures for travellers were based on the scientific evidence available.
It said judgements were made on how best to keep people in Scotland safe.
Mr Shapps also said that adding Portugal to the list had caused “confusion” and that Scotland and Wales had not taken the latest data into consideration.
Quarantine for travellers coming from Portugal begins at 04:00 on Saturday.
French Polynesia was also added to the list from 04:00 the same day.
‘Jumped the gun’
Speaking on the BBC’s Today programme, Mr Shapps said: “On Wednesday the Scots – without using the joint bio-security centre data for this particular decision – decided that people from Greece would be excluded, and jumped the gun on that.
“It is their right to do it but it doesn’t make the overall message any clearer.”
The quarantine rule for travellers coming to Scotland from Greece came into force at 04:00 on Thursday.
The ruling also affects those coming in to English airports from those countries on the list, before travelling to Scotland.
Mr Shapps said “ideally” the UK government would try to co-ordinate with the other administrations on travel announcements but that this week “it didn’t work out”.
The UK is now split on its rules for Portugal. Quarantine for Welsh travellers began at 04:00 on Friday, Scots have to self-isolate from 04:00 on Saturday and English returners are not subject to any requirements to self isolate.
Portugal, Greece and French Polynesia are still on England and Northern Ireland’s lists of travel corridors.
Mr Shapps also claimed that the Scottish and Welsh governments may have made decisions on Portugal without seeing all the data.
He said: “The Welsh administration had not noticed or not seen a second figure which is the percentage number of cases which test positive. That is really important because what we don’t want to do is exclude countries for doing the right thing in carrying out lots of tests.
“When we brought Portugal into the travel corridor they had a test positivity rate of 1.8% but this week it was 1.6%, so the number had fallen.”
He described Portugal as being on a “borderline”, adding that “the opinion of England and Northern Ireland is that it did not justify quarantine this week”.
The seven-day infection rate in Portugal has increased from 15.3 to 23 per 100,000 people.
A seven-day rate of 20 per 100,000 is the threshold above which the UK government generally considers triggering quarantine conditions.
Holidaymakers have only been able to travel from Scotland to Portugal without quarantine restrictions since 22 August, when it was added to the government “exemptions” list.
The Scottish government said that sometimes its decisions differed from those made by the other three governments.
A spokeswoman said: “In the case of Greece, we had a worrying number of people in Scotland who tested positive for Covid-19 and who had returned from Greece within seven days of the onset of symptoms. We could not afford to ignore that growing threat to public health.
“In the case of Portugal, it was unfortunate that the UK government announced their decision yesterday before ministers from England, Scotland and Northern Ireland met and before considering the latest Joint Biosecurity Centre data. This indicated a significant rise in both the prevalence of the virus in Portugal and in test positivity.”
The quarantine developments have been criticised by leading figures in the aviation industry, who have compared job losses in the industry to the demise of the coal industry in the 1980s.
Mike Tibbert, vice president of Scottish Passenger Agents’ Association (SPAA) accused the Scottish government of playing games, with its “half announcements and teasers”
He said: “The entire travel sector and the travelling public need consistency and clear, well timed messaging.
“But the toing and froing on the safe list versus quarantine is actually distracting from the main issue which is the total lack of immediate support for the travel sector and the complete absence of a strategic plan to save future travel.
“Once lost, our connectivity to the rest of the world – and consequently theirs to us – will disappear.”