Mark Sampson, the manager of the England women’s football team, is alleged to have told one of his black players to make sure their Nigerian relatives did not bring Ebola to a game at Wembley, according to extraordinary new evidence the Guardian can present as part of the Eni Aluko hush-money case.

Aluko tells this newspaper that the Football Association has known about the comment – described in one letter from the Professional Footballers’ Association to the governing body as a “racist joke” – since November 2016 but chose to ignore it despite a previous allegation that Sampson had asked a mixed-raced player in another England get-together how many times she had been arrested.

An internal investigation cleared Sampson of any wrongdoing in relation to the first alleged remark – “Haven’t you been arrested before? Four times isn’t it?” – and an independent inquiry, commissioned by the FA and overseen by the barrister Katharine Newton, later reached the same conclusion. That decision, however, has been described by Aluko as a “farce” at a time when the FA has been forced to admit the mixed-race player was not interviewed for either investigation. Newton’s investigation cleared Sampson of a number of allegations made by Aluko.

Aluko, who was born in Nigeria but moved to England with her family as a young child, was paid £80,000 by the FA to sign a confidentiality agreement but has now obtained consent to tell her side of the story and in an interview with the Guardian she alleges that Sampson made the comment to her about Ebola before England played Germany in November 2014.

“We were in the hotel. Everybody was excited. It was a big game. On the wall, there was a list of the family and friends who were coming to watch us and I just happened to be next to Mark. He asked me if I had anyone who would be there and I said I had family coming over from Nigeria. ‘Oh,’ he said. ‘Nigeria? Make sure they don’t bring Ebola with them.’

“I remember laughing but in a very nervous way. I went back to my room and I was really upset. It might have been easier to take if it was about me alone. Lots of things had been said about me over those two years but this was about my family. I called my mum and she was absolutely disgusted.”

Sampson is understood to deny making the alleged Ebola remark but, according to the FA, is not planning to say anything at this time.

The FA was notified about the alleged incident in a letter from the PFA in November 2016 that described the internal inquiry as “not a genuine search of the truth” and “a sham which was designed to establish the truth but intended to protect Mark Sampson”. The FA has accepted receiving that letter but says it was not a formal allegation, hence the lack of investigation.

Eni Aluko, in action for England in 2016, says: ‘I can recognise something toxic when I see it.’ Photograph: Nick Potts/PA

Aluko also alleges that one member of staff repeatedly spoke to her in a mock Caribbean accent – another allegation that was put to the authorities in the same letter – and the FA is likely to face even more scrutiny because of its explanation about why it did not interview the mixed-raced player over the arrests allegations.

According to the FA, it did not know the player’s identity because Aluko did not name which team-mate it was. Yet Aluko’s original complaint made it clear who it was, stating the incident happened at the China Cup in October 2015 and involved a mixed-race midfielder – the only one in the squad – who was new to the England set-up, had been raised in London, and even naming the club for which she played.

The Guardian’s inquiries discovered the player’s identity by applying a simple search of the FA’s website, but we have chosen not to name her after a request from the player and her club. “The most basic investigation, if they really wanted to find the truth, would have found out who it was,” Aluko says. “They could have got her name in minutes if they really wanted the truth.”

The most basic investigation, if they really wanted to find the truth, would have found out who it was

In an interview that threatens to go to the top of the FA, Aluko said: “She has put it in writing to confirm it happened. Yet the FA has had two investigations and nobody has been in contact with her. They were having an investigation but they did not bother to speak to the person to whom a comment with racial connotations – in my opinion – was made. I think that’s pretty astonishing. Can you imagine, thinking back to when Roy Hodgson [as manager of the England men’s team] made the comment about the ‘space monkey’, if the FA had an inquiry, clearing him of any wrongdoing, but without bothering to speak to Andros Townsend, the player he was talking to? Well, that’s what has happened in this case.”

The FA has also accepted that the initial findings, throwing out Aluko’s complaint that she had been the victim of bullying and discrimination, were delivered to her before the inquiry had even spoken to one of the players, Lianne Sanderson, who had been named as a key witness. The official explanation from the FA is that it was handled in that order because of timings and logistics, as well as the PFA applying pressure for it to be a quick process. The FA says Sanderson’s evidence played a part later on for the final internal report. Aluko’s case is that this is further evidence to show the inquiry was a “farce”.

Sampson has previously disputed the allegation about the China Cup and Newton’s report exonerates him, saying she did not find any evidence that it was said and had watched a video recording of the relevant meeting. The FA, according to Aluko, will not pass over that video.

Aluko goes on to say that her 11-year England career, encompassing 102 caps, was ended within a week or so of detailing her experiences in what was described as a confidential report for what the FA’s technical director, Dan Ashworth, called a “culture review”. Sampson is said to have visited her at Chelsea’s training ground and said he was dropping her for “unlioness behaviour” on the previous England camp. Her view is that it was “retaliation” but the FA has told her the two are not related. According to Newton’s report, Sampson’s explanations for leaving out Aluko related to her attitude and behaviour.

Aluko then received an email, within 24 hours of another meeting with leading FA executives to discuss her complaint, that the organisation was holding an investigation into her work as a sports lawyer for a football agency. Aluko questions whether it was another coincidence or “something far more sinister” and believes there is a direct link as to why she has been frozen out of the England squad despite winning the Golden Boot as the leading scorer in the country last season. Newton accepted the timing of the investigation into Aluko’s work was “unfortunate” but did not consider it “in any way a retaliatory act” or to be related to race. The FA says it investigates any player involved in intermediary activity and asks them to stop.

“I believe all these things are happening because it’s a conversation about race and this is a big problem in the world right now,” Aluko said. “Herman Ouseley [the chairman of Kick It Out] said it. On the pitch there are clear punishments when it comes to issues involving race. Behind closed doors, we don’t know the FA processes.

“We do know [the mixed-race player] has not been picked since this incident. Lianne Sanderson hasn’t been picked since she complained about why her 50th cap was forgotten on the same trip that the 100th cap of a white player was remembered. Lianne asked: ‘Why me?’ The 50th cap is a customary celebration. It’s standard. There is a presentation in front of the team and you have a special shirt with ‘50th cap’ written on it. It’s a big deal. She asked why she had been forgotten and she hasn’t been picked since.

“Anita Asante disappeared without trace despite playing for one of the best teams in Europe. Danielle Carter scored two hat-tricks for England and doesn’t get picked any more – why? There are lots of national teams that are very white, not just England, and I’d hate to say we should be picked because we’re black or mixed race. But are we all bad characters? Are we all terrible players? That’s the question I think people need to be asking because a pattern is emerging here, as clear as day, and my belief is that it’s a culture.

“For months, one member of staff used to talk to me in a fake Caribbean accent. He thought it was OK to do that, he thought it was funny. I believe he was empowered to do that because of the culture. We pleaded it [in submissions to the FA] but they chose to ignore it.

“Yes, in a football environment industrial language is used. I’ve been at Chelsea five years and been the butt of many jokes. And I give it back sometimes. That is the beauty of team spirit in a healthy dressing room. I’m not a sensitive, precious person. I’ve been in the [England] team for 11 years, I’ve been through ups and downs. I’ve played for boys’ teams. I’ve played for Chelsea, at the top level, and I’ve been dropped by Chelsea before but I can recognise something toxic when I see it. This is a culture that has systematically dismissed certain players. There is lots of talk about being the most together team in the world – I’ve truly never felt so isolated as I was in that team between 2014 and 2016.”