The region, which includes Surrey, Hampshire and Kent, has seen a sharp rise in cases in recent days.
The total number of cases over two weeks needs to be below 30 cases per 100,000 of population for seven days to stay to qualify for Guernsey’s category two, which allow arrivals to be released from quarantine after testing negative on arrival.
Under category three restrictions, travellers must self-isolate for at least seven days.
The south-east moved to the watchlist last week after going above 30.
Over the last seven days its numbers have risen from 33 cases to 49 cases.
South-east had only been in category two since mid-May.
This move leaves the south-west as the only English region in category two.
Numbers there have risen from 18 cases per 100,000 to 23 over the last seven days.
Overall England’s case numbers have been rising, with the country going from 57 cases per 100,000 to 76 in the last week. The numbers were last that high in early April.
However they are still much lower than at the height of the second wave in January, when the prevalence was more than 1,000 cases per 100,000 people.
Aurigny operates services to Southampton and Gatwick, which are both in the south-east region, as well as Manchester.
Before the pandemic those routes were some of the busiest through Guernsey Airport.
An airline spokeswoman said customers were aware that categories could change at short notice, and that was why it was offering an assurance programme, to allow travellers to move flights or get vouchers.
However not many people have had to move their flights in light of the latest news.
‘I think people are still booking very last minute,’ she said.
‘We had a lot of people travelling last week for half-term, but that has finished now.’
Guernsey uses a 14-day total, while Public Health England uses a seven-day total, leading to different figures to calculate prevalence rates.