The FA has rejected what it calls "substantial and serious inaccuracies" put forward by Kick It Out's head of development Troy Townsend in a documentary about Anton Ferdinand's high-profile racism case against John Terry.
In Anton Ferdinand: Football, Racism and Me, which aired on BBC One on Monday night, Ferdinand speaks to Townsend to ask why Kick It Out did not do more to help him when he brought his case against Terry in 2011.
In the programme, Townsend tells Ferdinand that rules prevent Kick It Out from speaking to an alleged victim while the case is active, something the FA said was not true.
Townsend told Ferdinand: "When an incident happens, I'm not supposed to talk to you. I'm not supposed to support you because football rules say I would be impeding an investigation. Basically what you're saying is you're hanging the victim out to dry until the end of the investigation."
In a statement issued after the programme aired, the FA said: "The FA has a longstanding relationship with Kick It Out and they remain one of our main stakeholders in the game as we share the ambition of eradicating all forms of discrimination from English football.
"Open and honest dialogue between both parties is key, as it always has been, and we will continue to work closely with them going forward.
"However, we can confirm that there are no rules or inferences in the relationship which prevent Kick It Out from contacting victims of discrimination.
"On the contrary, The FA's written policy is to actively encourage the involvement of Kick It Out so that they can support victims of discrimination during and after The FA's disciplinary process.
"Kick It Out has been present and provided support to players involved in discrimination investigations in the past and would be encouraged to continue to play this role going forward also."
Additionally, Townsend told Ferdinand he felt that, because Kick It Out receives its funding from the game's governing bodies, including the FA, they are put in an awkward position when criticising the authorities.
"I feel every time I speak I put my job at risk," he said. "When you're criticising the authorities, they don't take too kindly to it. Remember we're criticising about a particular topic that we should all be concerned about, we all want to do better at.
"That's why I continue to feel, are we taking the situation and stories about discrimination and racism seriously, or are we continuing, nine years on, to pay lip service?"
The FA's statement said: "In alleging that an individual at Kick It Out fears losing their job if they criticise footballing authorities, this is simply without foundation.
"No player, or any other participant who is the victim of abuse of any kind, should feel that they are not able to access the support that they need.
"We strongly condemn all forms of discrimination and we take all complaints seriously. As English football's governing body, we have a responsibility and a duty to investigate all incidents and allegations that we are made aware of.
"Tackling discrimination is core to the values of The FA and we work closely with our stakeholders across the game and the relevant authorities to take action against anyone who is found guilty of an offence.
"We remain fully committed and focused on driving out discrimination from the game and ensuring that English football is a diverse and inclusive game for all."
