The holiday hotspot, including the islands of Madeira and the Azores, will be removed from the green list exempting the need to quarantine on return from 4am on Tuesday.
But Portuguese ministerial social media account said that they “cannot understand” the “logic” of the decision amid fury from holidaymakers.
Soon after the changes were revealed, the account of the cabinet of Portugal’s Minister of State for Foreign Affairs tweeted in English: “We take note of the British decision to remove Portugal from the travel ‘green list’, the logic of which we cannot understand.
“Portugal continues to carry out its prudent and gradual deconfinement plan, with clear rules for the safety of those who live here and those who visit us.”
People returning to the UK from Portugal will be required to self-isolate at home for 10 days as part of coronavirus restrictions.
Many holidaymakers in Portugal face a scramble for flights home before the new rules are introduced.
The news was met with outrage from both travellers and service providers with EasyJet’s chief executive Johan Lundgren describing it as a “shock decision” and a “huge blow” to Brits currently in Portugal.
Andrew Flintham, the managing director of the TUI UK travel group, blasted the announcement as “another step back for our industry”.
While Virgin Atlantics boss questioned the Governments strategy.
Shai Weiss said: “We are yet to see clear and transparent guidance on the methodology and data the Government is basing these decisions on. It shouldn’t be a state secret.”
Some airlines have even delayed or halted their flights. Airline Jet2 delayed the restart of its flights and holidays from June 24 to July 1 following the changes to the travel list.
Labour criticised the “chaos” as reports about the restrictions dripped out of the Government ahead of official confirmation and travel bosses said the move will cause “untold damage to customer confidence”.
Shadow home secretary Nick Thomas-Symonds said: “The confusion over the ‘amber list’ has led to reports of over 50,000 people travelling to the UK daily, with only a tiny percentage going into hotel quarantine and a stream of flights entering the UK from ‘Amber List’ countries.”
He went on: “Moving Portugal onto the ‘Amber List’ is not the answer. The ‘Amber List’ itself should be scrapped.”
Portugal’s seven-day rate of coronavirus cases per 100,000 people stands at 37.2, up from 30.7 a week earlier.
The announcement came as Public Health England said the Covid-19 variant that originated in India was now believed to be dominant in the UK, with early evidence suggesting it may lead to an increased risk of hospital admissions compared with the Kent variant.
It also comes on the same day the Government said a further 5,274 lab-confirmed cases of coronavirus had been recorded in the UK as of 9am on Thursday, the highest single-day figure since March 26.
A total of 12,431 cases of the Indian variant, also known as the Delta variant, have been confirmed in the UK up to June 2, according to Public Health England (PHE), which is up 79% from the previous week’s total of 6,959.
Dr Jeff Barrett, director of the Covid-19 Genomics Initiative at the Wellcome Sanger Institute, said the Nepal mutation (B.1.617.2 with an additional mutation: K417N) of the variant first detected in India (B.1.617.2), has also been observed in other variants including the one first identified in South Africa.
He said it “is believed to be part of why that variant (South African) is less well neutralised by vaccines”.
Dr Barrett added that because of this possibility and because the Indian variant appears more transmissible than the variant first detected in South Africa, scientists are monitoring it carefully.
He explained this Indian variant plus the K417N mutation has been seen in numerous countries, including the UK, Portugal, the USA, India, Nepal and Japan.