The hub was launched by Mr Khan with the Met Police in April 2017. Figures obtained by the PA news agency showed that just 17 out of 1,851 reports (0.92%) resulted in charges.
Only seven of these led to prosecutions, though there were 59 other positive results such as cautions and harassment warnings.
The low number of charges is thought to be due to the high Crown Prosecution Service charging threshold for online hate, and the difficulties investigators face in obtaining information from social media companies.
But Tory Susan Hall, a member of the London Assembly, which holds Mr Khan to account, described the project – which has been given a budget of more than £1m since 2017 – as “an exercise in spin over substance”.
She said: “With Sadiq Khan’s online hub delivering disappointing results and hate crime on the rise, it is clear that the mayor is failing to drive this disgusting discrimination and abuse out of our city.
“True to form, the mayor’s online hate crime hub has been an exercise in spin over substance. Khan can talk a good game and grab the headlines, but time after time he fails to deliver the change that London needs.
“The money splurged on this project could have been used to invest in additional police officers and protect Londoners from a whole host of crimes, including hate crime offences.”
A spokesman for Mr Khan said: “The mayor takes a zero-tolerance approach to hate crime in London and the hub is supporting victims and helping us respond to the growing threat that London’s diverse and minority communities are facing both on and offline.
“The Met has made huge progress in tackling all forms of hate crime but it’s clear more needs to be done.
“The police have City Hall’s full support in enforcing the law against anybody who commits these crimes.”
Hate crime offences recorded by police forces in England and Wales hit a record high last year, with 103,379 in 2018/19 – up 10% from the previous year and more than double the 2012/13 figure of 42,255.
Home Office statistics do not distinguish between crimes committed online and offline.
Additional reporting by PA.