Jet2 has delayed the restart of flights and holidays following the Government changes to travel lists on Thursday.
The firm's boss called for "openness and transparency" on coronavirus data so that the industry could better understand decisions affecting airlines and their customers.
It comes after several changes to the travel lists - including moving Portugal from "green" to "amber" - were made by the Scottish Government on Thursday.
Jet2 said in a statement: "Following today's update, we have taken the decision to restart flights and holidays on July 1 2021.
"For any destinations currently on the Amber List, we are also allowing customers to amend their booking free of charge if they are due to travel between July 1 and July 21 2021."
Steve Heapy, CEO of Jet2.com and Jet2holidays said: "We know how disappointed our customers and independent travel agency partners will be following today's announcement, and we share their concerns and frustrations.
"We are now calling for complete openness and transparency when it comes to the data, so that customers and the industry can really understand what is driving these decisions."
"We agree that public health must be the number one priority. However, despite all the evidence and data showing that travel can restart safely and at scale, the UK continues to remain largely grounded whilst the rest of Europe opens up."
Jet2 said flights to Turkey, which remains on the "red" list, would not restart until July 22.
It added that customers affected by changes to the programme would have their bookings automatically cancelled and would be given a full refund.
Portugal was moved from the 'green' to 'amber' list in the first review of the international travel restrictions since the traffic light system was introduced on May 17. It's subject to review every three weeks.
Transport Secretary Michael Matheson said: “Portugal is a popular destination for Scottish holiday makers and this change will clearly cause disruption to people’s travel plans.
“However we have been forthright from the outset that the traffic light system is designed to protect the safety of the people of Scotland and the continued progress we are making as we come out of lockdown.
“Using the stringent methodology of the Joint Biosecurity Centre it is clear the risk this new variant poses is now too great to allow unrestricted travel to Portugal, an approach that has been agreed by all four nations.
“International travel for holidaying purposes remains risky and subject to sudden change. We have said before people should think very carefully about travelling – and this latest development serves to underpin that advice – especially so given the prevalence and unpredictable nature of variants of concern.”
