The UK's biggest tour operator, Tui, has suspended all flights from Spain and the Canary Islands scheduled to leave on Sunday.
Andrew Flintham, managing director of Tui UK and Ireland, made the announcement on Saturday evening hours before new rules came into force for UK travellers.
It comes after the government added Spain and the islands to its list of at-risk countries.
This means holidaymakers arriving back from Spain, the Canaries and the Balearic Islands face the prospect of isolating for two weeks from midnight into Sunday.
Britons have been advised against all but essential travel to mainland Spain by the Foreign Office – though this part of the guidance does not apply to the Canaries and the Balearics.
While Tui has cancelled flights, easyJet and British Airways are planning to continue operating as normal over the coming days and easyJet said that people no longer wishing to travel could seek to transfer their flights without a fee or receive a voucher.
Tui's Mr Flintham assured passengers who are currently on holiday that they will be able to return on their intended flight home, while others would be contacted by Tui to arrange refunds or rebookings.
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He said: "We're incredibly disappointed that we didn't get more notice of this announcement, or that this decision wasn't made yesterday, as many Brits travel on holiday at the weekend.
"We also look to understand why quarantine has been issued for a whole country, including the Canary Islands and Balearic Islands, when the travel advice isn't aligned (only applying to mainland Spain). It demonstrates why clear regional travel corridors need to be considered.
"The health and safety of our customers and colleagues is always our highest priority and welcome travel advice that protects those that holiday with us.
"However, the UK government must work closely with the travel industry as this level of uncertainty and confusion is damaging for business and disappointing for those looking forward to a well-deserved break."
The new rules were announced by the Department for Transport, with the government asking employers across the nations to be "understanding" of workers who need to self-isolate.
Transport Secretary Grant Shapps may also have to quarantine as he is currently away on holiday in Spain.
Mr Shapps is understood to have flown out on Saturday morning when the travel corridor with Spain remained open, but the government has since taken the decisRead More – Source