He went on to say that 80,000 Volkswagen engines that had been fitted with the ‘defeat devices’ were registered in the capital.
The devices were able to detect when the vehicle’s engine was in a test scenario and could subsequently alter performance to improve the car’s results.
VW is the world’s largest carmaker, and they owned up to fitting around 11 million cars across the globe with the cheating software.
Transport for London worked out the £2.5 million figure from the amount of VW owners, who claimed a discount for which they were not eligible.
“If you don’t ask you don’t get. I’m a champion for clean air, I’m a champion for London,” said Mr Khan.
“Londoners, in good faith, bought these vehicles. They weren’t clean. We’ve lost revenues from the congestion charge, they’ve got a case to answer.”
Vehicles involved in the scandal include the Audi A1 and A3, Skoda Fabia and Octavia, Seat Ibiza and Leon and VW’s Golf and Polo vehicles.
In a statement made to the Sunday Times, the German car maker said: “Volkswagen products perform well in independent real-world emissions testing against new cars in general.
“It is therefore difficult to understand why our products might be singled out for pollution penalties.”
The controversy was discovered in September of last year, after the US’s Environmental Protection Agency (EPA) found a number of Volkswagen vehicles being sold in the States contained software that could detect test conditions, and could adjust performance to improve results.
The car maker has subsequently admitted cheating in emissions tests.