People arriving in the UK from Portugal after 4am on Tuesday will need to self-isolate at home for 10 days after the Government moved it from the green list to the amber list.
A seat on a Ryanair flight from the capital Lisbon to Manchester on Monday costs £339, whereas travel on the same route is available for just £75 on Wednesday.
British Airways is charging £348 for flights from Faro to London Heathrow on Sunday and Monday, but the price drops to £137 on Tuesday.
EasyJet is operating larger aircraft and more flights to bring people back to the UK while British Airways has also increased its schedule.
Tui, the UK's largest tour operator, said it has 9,500 customers in Portugal but that was already due to have fallen to 2,000 by Tuesday because of the end of half-term for schoolchildren.
A spokeswoman told the PA news agency that half its customers with Portugal bookings for June have amended their trip - mostly until summer 2022 - while the other half plan to go ahead with it despite the quarantine rules.
"There is a lot of bewilderment and real frustration and confusion about what is happening," she added.
The firm is allowing consumers to change dates in response to Portugal moving to the amber list, but is not offering refunds as the Foreign, Commonwealth and Development Office does not advise against travel to the country.
The requirement for travellers to take a coronavirus test in the three days before a flight to the UK departs is also creating difficulties for people in Portugal.
Property developer Simon Smith from Stamford, Lincolnshire, is currently in the Lagos area with his wife and two young children.
He hopes they can fly home on Saturday, earlier than planned, but they have been unable to get tested despite visiting five medical centres and the region's main hospital.
He was turned away from one centre after it ran out of testing kits.
"There were about 35 people in the queue, all British, and they told us, 'the first 15 are okay, but the rest of you might as well go home because we don't have enough tests', he told PA.
The family has been told the airport has a small amount of Covid tests available, so plan on turning up to their flight five hours early in the hopes of getting one.
"If we can't get that, we can't fly", he said. "I have meetings on Friday, I can't afford 10 days' quarantine, it is a joke."
More positive news came out of France, which has relaxed its travel rules to allow tourists from much of the world into the country from June 9, including the UK, providing they are fully vaccinated or have proof of a negative test.
However, France remains of the UK's amber list, meaning tourists would still have to self-isolate at home for 10 days upon their return.
A Portuguese epidemiologist claimed the decision to move Portugal to the amber tier was "an overreaction".
Professor Henrique Barros, president of Portugal's National Health Council, said the country's overall coronavirus situation is "relatively stable".
He made the comments after Communities Secretary Robert Jenrick said positive cases had doubled in the last three weeks in Portugal.
Prof Barros told Sky News: "We didn't reach such an increase, except as I said in a specific area around Lisbon.
"The overall picture in the country, we didn't reach such figures."
The decision to move Portugal to the amber list means people returning to the UK from there must self-isolate at home for 10 days.
"I think it's an overreaction," Prof Barros said.
The health chief explained that the rise in infections are mainly among people aged under 40, and there is a "very low incidence of cases" in the over-50s.
He stressed that hospital admissions at the present time are "very low", at less than 25 people per million.
Officials in the country "pay a lot of attention" to monitoring the virus, he added.
Mr Jenrick acknowledged that the situation was "frustrating" for travellers, but insisted the Government was "clear" that the classification of green list countries could change.
"Those countries are being reviewed every three weeks, and so there was always a risk with a fast-moving situation with new variants that countries might either go on to that list, or indeed come off," he told Sky News.
The Cabinet minister said the movement of Portugal to the amber tier was partly due to "growing evidence of a further mutation being called the Nepal variant".
He revealed "we don't yet know how much of a problem that is" but insisted it is "important that we take a cautious approach".
Julia Lo Bue-Said, chief executive of travel agent group Advantage Travel Partnership, said the decision in relation to Portugal was "an absolute devastating blow" for consumers and the industry.
She told BBC Radio 4's Today programme: "It now throws confidence completely out of the window."
She added: "It puts the industry in a really difficult position and consumers in a difficult position in order to be able to plan effectively."
Portugal is not the only country which moved on the traffic light rating system on Thursday.
Afghanistan, Bahrain, Costa Rica, Sudan, and Trinidad and Tobago have also been placed on the red list, meaning people arriving in the UK from those nations must stay in a quarantine hotel for 11 nights.
Reporting by PA