The Prime Minister unveiled his battle plan on Tuesday to tackle the illness sweeping across the globe after chairing a Cobra meeting on Monday.
But the London mayor, who has now launched his re-election campaign, hit out at Mr Johnson for excluding him from the meeting that agreed upon a Government strategy for tackling Covid-19.
He pointed out that London is served by the UK’s biggest airports and a population that swells to more than 10 million with tourists and commuters during the day.
“Dealing with the coronavirus is more important than party politics and it’s really important we put aside petty differences and all work together,” Mr Khan told reporters after Tuesday's campaign launch in Hackney.
“I will be looking at what the Government’s announcement is, I don’t know what they are.
“It just seems a bit odd for the Government not to include us when it comes to either Cobra or when it comes to planning and preparation. It’s for the Government to explain why they want to exclude us.”
Downing Street declined to comment on why Mr Khan was not included.
The government’s plan for a worse-case scenario, published following Monday’s meeting, includes measures such as instructing police to ignore low-level crime, drafting in the army and warns that up to a fifth of employees could be absent from workplaces.
Mr Khan said on Tuesday that he could not currently envisage a need to shut the Tube or discourage the use of public transport, as he examined the action plans of other cities such as New York.
“I’m confident of the advice we are receiving, the advice is (that there is) no reason at all to worry about using the Tube or buses,” he told journalists.
“I don’t foresee a situation where we are advising people to not use the Tube or public transport but we review this at each stage.
“I don’t foresee a situation where we do what other cities have done and say don’t go to concerts and ban people from confined spaces.”
The Labour mayor also revealed that he is avoiding shaking hands with anyone in an attempt to protect himself from the illness that has seen some 90,000 people infected and killed more than 3,000 people worldwide, most of those in China.