It comes after the Government quietly released fresh guidance for eight Indian variant hotspots, without consulting town hall chiefs.
The new advice to control the variant advises people from Hounslow, Bedford, Blackburn with Darwen, Bolton, Burnley, Kirklees, Leicester and North Tyneside not to meet inside if possible, in contrast to the most recent relaxation of rules.
It also urges people to avoid travelling in and out of the affected areas unless it is essential.
In a statement, Mr Khan said he had met with vaccines minister Nadhim Zahawi, alongside mayors from across the country to discuss the matter.
He said: “I raised the need for clarity on the Government’s guidance and support for those living and working in Hounslow, and also the impact of new guidance on Heathrow airport.”
The Mayor was referring to the fact that the airport falls under Hillingdon borough, bordering Hounslow and according to the council, some 11,000 residents have jobs directly linked to the airport.
Mr Khan also added that surge testing in the borough, which currently has an infection rate of 56.3 per 100,000 people, was already taking place and more vaccines are being made available.
“It’s vital that anyone who is offered a test or a vaccine takes it as soon as possible. I also continue to urge the Government to increase the availability of the vaccine to younger age groups where this variant is spreading.
“We’ve worked hard to reduce the number of cases in London but I’m confident that by all doing what we can to reduce the spread of this variant, we will get over this latest hurdle,” he continued.
The comments came hours after Cllr Steve Curran, Leader of Hounslow Council, tore into the governments decision - calling it “ridiculous.”
He added: “It is unbelievable that new guidance came to light only by checking the Government website.
“To date I have received no communication at all from the Government. This is another example of the left hand not knowing what the right hand is doing. It’s shambolic.”