Passengers permitted to fly from places with high levels of coronavirus infection will go through a specific arrivals facility at the west London airport.
It comes amid concern about overcrowding at Britain’s largest airport, with possible health implications for staff and passengers.
A Heathrow spokesman said: “We’re adapting Heathrow to this longer-term reality by initially opening a dedicated arrivals facility in Terminal 3 from June 1 for red list passengers arriving on direct flights.
“We will move this facility to Terminal 4 as soon as operationally possible.
“While opening this facility will be very challenging logistically, our hope is that it will enable Border Force to carry out its duties more efficiently as passenger volumes increase in line with the green list.
“Until then, the current red list system will remain in place.
“This system has been designed by the Government and has several layers of protection to keep passengers and colleagues safe – including mandatory negative Covid tests for all international arrivals, mandatory use of face coverings, social distancing, segregation and enhanced cleaning regimes and ventilation in immigration halls.”
The decision was welcomed by the GMB union.
Nadine Houghton, its national aviation officer, said: “Heathrow has done the right thing and provided a dedicated arrivals area at T3 for red list travellers.
“Ministers still need to explain how infrastructure will cope if more countries are added to the red list and we will be seeking assurances from the Government on this.”
Currently people arriving from a red list country must enter a quarantine hotel.