The ads, which have been spotted across the capital, feature the slogan 'Facts don't lie. People do' and a link to the website MJInnocent.com.
It comes after one firm was forced to edit bacon and jam out of their advert because of a ban on junk food ads on the tube, which was championed by Khan.
Twitter users have hit out at the Labour mayor and Transport For London for allowing the posters, with some accusing him of having double standards.
One tweeted: "I can imagine that @SadiqKhan would step in if someone put an advert on a bus saying 'Bombs don't kill people. Muslims do'.
He'll quite happily allow adverts calling abuse victims LIARS. This is not okay
"But when it comes down to Michael Jackson, he'll quite happily allow adverts calling abuse victims LIARS. This is not okay."
Fans used crowdfunding websites to get cash for the Jackson adverts in response to the Leaving Neverland documentary, with over £14,000 raised so far.
In the film, which aired this week, accusers Wade Robson and James Safechuck say they suffered abuse in Jacko's enormous California mansion he called Neverland.
'DOUBLE STANDARDS'
The adverts feature a black and white photo of the singer with his mouth covered with the word “innocent” above a link to MJInnocent.com.
They first appeared on February 25 and will been on London buses until March 24.
Other Twitter users criticised the mayor for allowing what they said is "victim blaming".
One posted: "@TFL Shocked and Saddened by your irresponsible advert on the side of a bus in support of #MichaelJackson. Triggering, silencing and feeding into rape myths. Disgraceful on a public service."
Another said: "Adverts maintaining Michael Jackson’s innocence against child sex abuse claims have been taken out on the side of London buses – pretty awful right? I’m surprised at @TFL for allowing this or getting in any way involved, it’s bizarre."
A TfL spokesperson said: “This advertising campaign is compliant with our advertising policy.”
A representative for the Mayor of London has been contacted for comment.
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