Employers are also concerned about how to ensure staff stick to the new isolation and holidaying rules.
Portugal, previously on the governments green list, has been moved to amber, meaning UK citizens should not visit the country on holiday and returnees must isolate for 10 days.
The decision was made due to rising coronavirus cases and concern over a Nepal mutation of the strain that first emerged in India.
The changes come into effect next Tuesday (8 June).
Trade union Prospect’s general secretary, Mike Clancy, said the travel news is further evidence of the instability facing the aviation industry this summer.
He said: “With government advice shifting regularly it is imperative that proper financial support for the sector is put in place.
“Even in the most optimistic scenario, we now face losing half of the summer before holidaymakers can confidently book travel to major destinations, and the nearer we get to the school holidays the more likely they will be to just stay at home.”
Clancy said the end of the furlough scheme in four weeks’ time will only add to the damaging uncertainty facing aviation.
“Ministers need to make clear that further support will be available to support jobs while restrictions on tourist travel remain in place.
“Without this, there’s a risk that the industry will no longer be there when restrictions are lifted,” he said.
Matt Jenkin, partner and head of employment law at Moorcrofts, said the changes to travel advice is likely to lead to workplace disruption as employees are required to quarantine rather than attend their workplace.
Speaking to HR magazine he said: “For employees who can work from home, employers should look to continue those arrangements on full pay.
“For those that can’t work from home, they have no entitlement to pay or SSP during this period so unpaid leave or taking additional holiday are likely to be options that will be considered.”
More countries were expected to be added to the list, giving hope to furloughed staff in the aviation and travel sector.
Andy Davies, senior vice president at HR software company MHR, said employees enjoying their holiday in Portugal are facing a dilemma if they cannot work from home over the quarantine period.
He told HR magazine: "Some employees may be given the option to take this time as paid holiday, however the reality is that for a lot of people this won’t be an option and they’ll be asked by their employer to take unpaid leave which may cause some financial hardship.
"The most benevolent employers will want to look after staff, but the most crucial part is that employers and employees should be communicating with each other to see what can be done to help one another.”