Kick It Out accepts "communication breakdowns" meant Anton Ferdinand did not receive the right assistance during his racism case, but says the bigger issue is its lack of capacity to deal with the flood of complaints it receives.
The Football Association said Monday night's BBC documentary about Ferdinand's racism case involving John Terry featured "substantial and serious inaccuracies" from Kick It Out's head of development Troy Townsend.
Townsend told Ferdinand that his organisation was unable to speak to victims of discrimination during an investigation.
He was banned for four matches and fined £220,000, having been acquitted in a criminal court.
Ferdinand said he "didn't feel like the victim" when he was being interviewed by FA investigators.
The FA said: "We fully respect Anton Ferdinand's recollection of the investigation and are saddened by his feelings during what was undoubtedly a difficult time for him.
"Notwithstanding the fact that the criminal case was unsuccessful, our regulatory team expeditiously progressed the disciplinary action both before and after the criminal case, which had to take priority.
"Believing in the case against John Terry, they worked tirelessly to ensure the case put before the disciplinary panel was robust, having appropriately recorded and challenged all relevant witness evidence, which ultimately resulted in a successful prosecution before an FA disciplinary panel.
"Early in the process, we also removed John Terry as England captain due to the seriousness of the allegations. It showed him no favouritism and made clear how serious the allegations were taken."