The government-funded project was attacked by the Sunday Telegraph for recording offensive messages posted on Twitter and Facebook as well as physical violence.
Of the 212 anti-Muslim incidents recorded by Tell Mama, 57% took place online, the newspaper reported.
Some of the incidents didn't take place in Britain and included in the tally were offensive remarks not directed at individuals but hate statements made publicly.
Tell Mama, whilst admitting the article was correct, labelled journalist Andrew Gilligan's evaluation as "reductionist" and said their figures would be independently checked by Birmingham university for a report next month.
The charity posted a point-by-point critique of the Telegraph's article online, arguing that many third party hate crime reporting organisations record reports of verbal abuse and "increasingly online abuse."
It also argued that graffiti in graveyards and broken windows on mosques are not 'relatively minor' but serve to impact on community tensions.
Online hate incidents should not be downplayed as they cause "emotional disturbance" and distress, Tell Mama added.
If figures from Tell Mama did not marry with police reports, this was because many Muslims "are fearful of engaging with police and many have reported to us that their cases have been re-classified with race hate incident flags rather than with Islamophobia flags" the detailed statement said.
However it did stress the United Kingdom was "still the safest place to live in and that it was one of the best countries for faith communities to be in."
The charity added: "Thankfully, there is something inherent within the British public which detests violence and this may be why we had not seen an orgy of violence after the murder in Woolwich."
On Saturday, the road outside the Palace of Westminster became a battleground as supporters of the British National Party (BNP) clashed with rival anti-fascist campaigners, predominantly members of Unite Against Fascism (UAF).