Greg Clarke’s position as chairman of the Football Association is likely to come under severe scrutiny after new revelations about his handling of the alleged‑racism scandal and cover-up that has led to his organisation being summoned to a parliamentary inquiry to explain the Mark Sampson affair.

Two weeks after Clarke publicly praised Eni Aluko for reporting alleged racism within the England Women’s football set-up, the Guardian can reveal his 14-word reply after initially being told of claims that the FA had put together an internal inquiry that was “not a genuine search for the truth” and “designed to close down the complaint and absolve Mark Sampson”.

Clarke was one of four senior executives to receive a six-page document from the Professional Footballers’ Association that accused the governing body of deliberately sabotaging Aluko’s 11-year international career to protect Sampson, the now-sacked England Women’s manager, and set out a series of grievances detailing “the incontrovertible evidence that makes it clear the purported investigation was a sham”.

The letter was sent in November 2016 and was also the first time the FA had been informed of a previously unreported allegation that Sampson – already accused of offending Drew Spence, a mixed-raced player, with an allegedly racist joke asking how many times she had been arrested – had made a comment about Aluko’s family and Ebola. That was later revealed to be a reference to Sampson having allegedly told Aluko to make sure her Nigerian relatives did not bring the virus to Wembley.

Sampson strenuously denies making any racial remarks about Aluko or any other player.

Yet Clarke’s response came in the form of a curt email that threatens to be hugely embarrassing for his organisation and leaves questions about his ability to run a body that purports to be leaders in the fight against racism.

Clarke is now under intense pressure to explain why he responded within 30 minutes, sending the PFA an email stating: “I’ve no idea why you are sending me this. Perhaps you could enlighten me?”

The one-line response has shocked a number of people who are working on the case and opened him to allegations that he completely misunderstood the seriousness of the matter at a time when the FA’s technical director, Dan Ashworth, and human resources director, Rachel Brace, had been accused by the PFA of conducting “a sham [inquiry] which was not designed to establish the truth but intended to protect Mark Sampson”.

The PFA, which was representing Aluko, was so taken aback by Clarke’s tone and apparent lack of interest it did not reply, taking the view that the man at the top of the FA should not need an explanation of why such serious allegations had been directed his way.

The latest revelations will raise further questions about whether the FA has treated the affair with the same seriousness as it would have done had it involved the men’s national team.

The Guardian sport front page on 22 August of this year. Photograph: The Guardian

Clarke’s handling of the crisis has already come under scrutiny because of the circumstances surrounding Sampson’s sacking and the latest revelations will further weaken Clarke’s position before his appearance alongside Ashworth, Brace and the FA’s chief executive, Martin Glenn, in front of the digital, culture, media and sport select committee on Wednesday. The relevant MPs have been made aware of Clarke’s email and he can expect some tough questions.

The four executives are likely to be asked to explain the safeguarding investigation that was cited as the reason for Sampson’s dismissal and how the people Glenn has described as “the grown-ups within the organisation” originally missed the report from March 2015 that stated its employee had inappropriate relationships with players at Bristol Academy, where he had previously coached.

However, the hearing was initially arranged to deal with the allegations of racism and cover-ups and Clarke will inevitably be asked why he appeared so uninterested in being told the FA had not dealt appropriately with allegations involving two female international players – including one who had won 102 caps but was dropped from the squad within two weeks of agreeing to discuss Sampson’s regime in the FA’s culture review.

The FA has declined to answer the Guardian’s questions about whether it was an appropriate response for someone in his position, or whether Clarke was willing to explain why he used such a dismissive tone given the seriousness of the allegations.

The FA also refused to answer questions about whether the latest controversy might have an impact on Clarke’s position or what it said about the organisation’s anti-racism policies that its own chairman should react that way when told of an alleged cover-up involving two seniorexecutives.

“Once Greg Clarke had received the letter he checked with his executive team as to what actions were being taken regarding the allegations,” the FA said in a short statement. “At this point there had been an internal inquiry and Katharine Newton was about to be appointed to lead an independent second inquiry. He was therefore satisfied that the FA was taking the matter very seriously and acting appropriately.”

Yet that still leaves serious questions about his judgment bearing in mind the correspondence from the PFA not only highlights the alleged Ebola remark but also states there was evidence that a member of Sampson’s staff allegedly used to talk to Aluko in a fake Caribbean accent.

Speaking on 2 October, Clarke praised Aluko for reporting Sampson. “I’m pleased she raised the issues. If there are issues, we want people to feel safe and raise them … all we want is to get to the bottom of it.”

Yet it was a different response to being informed by the PFA that Ashworth and Brace had been guilty of “gross failures”, not least by putting together their findings, exonerating Sampson of any wrongdoing, before speaking to one of the key witnesses and without watching a video recording of the relevant meeting in the 2015 China Cup where the comment to Spence was allegedly made. It was, according to the PFA, a “failure to conduct even a basic investigation”.

Ashworth’s role, in particular, is questioned bearing in mind his claims that it was merely a coincidence – the PFA uses the word “retaliation” – that Aluko, last season’s Golden Boot winner, lost her place in the England squad within a fortnight of what she was told was a confidential process. He also says it was a coincidence that the FA launched an investigation into Aluko’s work as a sports lawyer, citing a potential conflict of interest, within 24 hours of the meeting when she explained her grievances.

Ashworth denies breaking any confidences but it emerged over the weekend that he was criticised in an independent inquiry, conducted by the barrister Newton, after nominating himself as a witness, apparently to speak on Sampson’s behalf, in the review he was overseeing.

Ashworth told Newton he did not see it as a conflict of interest. Yet the barrister disagreed and the FA, already accused of one whitewash, might have to explain why this part of her findings was not included in the edited section the organisation later released. “An investigator should not also be inputting evidence into the same investigation and I would advise avoiding this situation arising in any future case,” Newton wrote.

Newton’s report also exonerated Sampson but ruled the comment to Spence had never happened without interviewing the player or three team-mates – Jill Scott, Izzy Christiansen and Jo Potter – who were in the same meeting. That will also form part of Wednesday’s hearing, not least because of the widespread scepticism surrounding the FA’s claims it did not know Spence was the player involved.

Amid escalating criticism of her initial three-month inquiry, Newton has now made it her mission to interview all the relevant players as part of a new investigation, reopened following the media coverage since the Guardian broke the story, on 16 August, about Sampson being accused of a racial remark. The latest investigation, the third in just over a year, has already begun and it is possible the initial findings could be delivered at the hearing.