The meeting in Whitehall brought together senior ministers and health officials and was designed to signal a step-change in the government’s response to the outbreak, agreeing an action plan to counter the spread of the disease.
It was the first in a series of weekly Cobra meetings attended by prime minister Boris Johnson, who has faced criticism for failing to take personal control of the UK’s response.
It is understood that representatives of devolved administrations were invited to dial in to the meeting, but when City Hall asked whether Mr Khan should attend they were told no.
The Mayor has attended earlier Cobra meetings on issues affecting the capital, such as terrorist attacks.
A City Hall source said: “People might feel it is a bit strange that he’s not invited given size of London, its status as a global travel hub, its large transport network and sports and entertainment venues.”
The prime minister's spokesman said Mr Khan was not invited because the meeting was meant to deliver a "a national response", while London - and other areas - were involved through local level resilience forums.
Join our commenting forum
Join thought-provoking conversations, follow other Independent readers and see their replies