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.
Kick It Out's executive chair Sanjay Bhandari said: "The FA are correct that there is an agreed protocol enabling Kick It Out to provide such support.
"Understandably, this includes provisions designed to preserve the integrity of evidence and thus maximise the prospects of a fair conclusion to the case.
"Due to communication breakdowns at our end, this has not been clearly understood at all times. Going forward, we are completely clear on that."
Bhandari added, though, that in his view there was a much bigger issue that needed to be addressed.
"We only have the capacity to support five to six players or grassroots participants per year. We receive over 500 complaints per year and we know that this is the tip of the iceberg," he said.
"We need to find scalable solutions to this problem. In the professional game, the primary welfare duty is on clubs as the employers.
"We would also urge any player to take advantage of the counselling and support services offered by the PFA and to use their support during an investigation. We need to find solutions for the scores of weekly victims at grassroots level where hate appears endemic."
On the documentary itself, Bhandari said: "The abiding feeling I was left with was one of profound sadness. Sadness at the visible and deep impact that the incident had on Anton and his family.
"And sadness that, as a game, collectively, we let him down. I hope that the process of creating the documentary helps Anton to reach closure on this painful episode in his life."
Terry was found guilty by an independent regulatory commission in September 2012 of racially abusing Ferdinand in a match between QPR and Chelsea the previous October.
The FA has provided an update following tonight's Football, Racism & Me documentary: https://t.co/fNvSGoWfIx. pic.twitter.com/oUVldYTfg4 — FA Spokesperson (@FAspokesperson) November 30, 2020
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."
