The new charge applies to most vehicles registered before 2006 that do not meet standards introduced in European Union countries in 2005.
Speaking to Sky News, Khan said: "We don't make a profit from the T-charge - it's costing us".
It will take the fee for pre-2006 vehicles entering London to 21.50 pounds (28.4 US dollars), costing some drivers who commute into London by vehicle more than 100 pounds a week (142 USA dollars).
The Toxicity-Charge - known as the T-Charge - is to be levied on top of the existing Congestion Charge of £11.50 for the majority of cars built before 2006. "The T Charge is a vital step in tackling the dirtiest diesels before I introduce the world's first Ultra Low Emission Zone as early as 2019".More news: Texas town offers hurricane relief, but only with a political promise
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About 438 schools in London are in areas exceeding legal air quality levels, according to the London mayor's office.
Khan said such polluting vehicles have made around 2.6 million trips within the London charging zone since January 2017.
"Filthy air is causing a public health crisis in the capital".
Green groups today welcomed the introduction of the T-Charge, but some warned more support is needed to encourage drivers to switch to cleaner vehicles.
Sue Terpilowski, a spokesperson for the Federation of Small Businesses, told the news site: "The introduction of the T-Charge comes at a time when small and micro-businesses in London are already facing astonishingly high property, employment and logistics costs".