UK Health Security Agency analysis suggested a strong indication of Omicron in Nigeria, said officials.
It means UK and Irish citizens and residents arriving from Nigeria must isolate in costly hotel quarantine for 10 days.
The Health Secretary, Sajid Javid, told broadcasters: “Since we have learned of this new variant our strategy has been to buy time. We have always said we will act swiftly should new data require it.
“Over recent days we have learned of a significant number of growing cases linked to travel with Nigeria.
He added: “Nigeria now is second only to South Africa in terms of linked cases to Omicron.”
All other travellers will be refused entry to England if they have been in Nigeria in the past ten days under the new rules.
This does not apply to those who have stayed airside and only transited through Nigeria when changing flights.
It comes after the UK introduced rules requiring vaccinated passengers arriving in the UK to take a day two PCR test and self-isolate until they receive a negative result.
From 4am on Tuesday, anyone travelling to the UK from places not on the red list are also being made to show a negative PCR or lateral flow pre-departure test.
The rules are next to be reviewed on December 20.
The Scottish and Welsh governments said they were both adopting similar ‘red list’ controls.
Anyone who arrived from Nigeria before Monday’s deadline is being “strongly” advised to isolate with their household for ten days.