Officials said the case was detected in a person who visited London but has since left the country.
UKHSA confirmed the individual had links to travel in southern Africa and had since been in the central London borough of Westminster.
Dr Jenny Harries, the UKHSA chief executive, acknowledged it is “very likely” that further cases of omicron, which is feared to spread rapidly and may evade existing vaccines to a degree, will be discovered in the coming days.
On Saturday, the first two omicron cases were discovered in Brentwood and Nottingham in individuals linked to travel to southern Africa.
The individuals who tested positive, and all members of their households, were told to self-isolate.
Cardiff Rugby has also said the team is unable to leave South Africa following two positive cases of Covid-19, one of which is suspected to be the omicron variant.
In a statement, the club said its players had returned to their hotel to isolate having been booked on to a flight set to depart on Sunday afternoon and it is now working with authorities to ensure the party’s safe passage home when appropriate.
Professor Neil Ferguson, the Scientific Advisory Group for Emergencies (Sage) member whose modelling helped instigate the first lockdown, said he expects to see “substantially larger numbers” of omicron in the UK in the coming days but welcomed the new measures as “proportionate” to slow the spread while scientists analyse its properties.
“That’s not to say we can be complacent, if we do see very rapid growth of omicron – and that’s a big if at the moment, and we have no guarantee we will – but if we do then, undoubtedly, I think the government would be wise to keep all options on the table in terms of how to respond to that,” he told BBC Radio 4’s The World This Weekend programme.
The variant has been identified in countries across Europe including Germany, Italy and Belgium, as well as further afield in Botswana, Israel and Hong Kong, since it was first reported to the World Health Organisation by South Africa on Wednesday.