Heathrow says it will be setting up a dedicated facility for passengers on direct flights from red list countries, following concerns that they were mixing with those from green and amber nations.
This facility will be set up in Terminal 3 from 1 June and will then be moved to Terminal 4 as soon as operationally possible.
Currently, all flights at Heathrow are operating from Terminals 2 and 5 following the temporary relocation of airlines from Terminals 3 and 4, amid the fall in demand for air travel due to the coronavirus pandemic.
A Heathrow spokesperson said: "Red list routes will likely be a feature of UK travel for the foreseeable future as countries vaccinate their populations at different rates.
"We’re adapting Heathrow to this longer-term reality by initially opening a dedicated arrivals facility in Terminal 3 from 1 June for red list passengers arriving on direct flights."
They added: "We will move this facility to Terminal 4 as soon as operationally possible.
"While opening this facility will be logistically very challenging, 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."
It comes after airport staff raised fears for their safety because of overcrowding, amid concerns that travellers arriving from red list countries are mixing with those from green and amber.
Travellers from different lists are stuck in a bottleneck before immigration, said the GMB union.
Heathrow says it is in negotiations with the government over the cost of the new facility.
Airport officials claim they need to recover some of the cost of it because it is government policy.
Heathrow says it has lost £2.4bn due to the pandemic and is suffering losses of £5m every day.
Bosses claim they have received limited financial support from the government and unlike retail businesses have had to continue to pay business rates in line with when they had 80% more passengers.
Earlier on Friday, Downing Street said it was up to airports to ensure those returning from red-list countries were separated from other travellers.
Asked about whether No 10 thought airports were doing enough to keep travellers from red list destinations away from others in UK border queues, a spokesman for the prime minister said:
"We’ve asked airports to make sure there are mitigations in place to make sure people can socially distance and, where possible, to allow people from red list countries not to have to intermingle with those who have returned from amber or green-list countries.
"But it is a matter for the airports to ensure provisions are in place."
Travellers arriving in England from red list countries need to isolate in a government-approved hotel for 10 days, as well as having a pre-departure COVID test, plus tests on day two and day eight of quarantining.
The government says people who have been in a country or territory on the red list in the last 10 days will only be allowed to enter the UK if they are a British or Irish national, or they have residence rights in the UK.
People should not travel to red list countries or territories, according to the government’s website.
Only travellers coming from green list nations do not have to quarantine, though they have to take a pre-departure test along with another test on day two after arrival.
Those from amber list countries have to isolate at home for 10 days, as well as taking a pre-departure test, and tests on day two and eight.