The Football Association is facing calls for an “open, transparent and independent investigation” into how it handled the Eni Aluko affair amid pressure from anti-racism groups and with Chelsea praising the player for coming forward with the allegation that Mark Sampson, the England women’s team manager, told her to make sure her Nigerian relatives did not bring Ebola to Wembley.

As Chelsea “commended” their forward and two other players, Lianne Sanderson and Anita Asante, expressed public support for their former England team-mate, the Professional Footballers’ Association has backed up Kick It Out’s request for the FA to start again with a new inquiry.

The Guardian can also reveal the PFA has expressed concerns about “suspicious activity” on Sampson’s Twitter account, where he was alleged to have made an unusual number of favourable references to Barack Obama, Serena Williams and Nicola Adams after the first allegation was made against him that he had asked a mixed-race player how many times she had been arrested.

Katharine Newton, the barrister who followed up the FA’s internal review with her own inquiry, has looked into the claims and her conclusion, seen by this newspaper, says she does not believe “the timing of the tweets are linked to any aspect of [Aluko’s] complaints” or that Sampson “has undertaken a cynical exercise in order to paint a picture of adulation of black athletes and politicians”.

Sampson denies making the Ebola remark and was cleared of wrongdoing by the FA in relation to the other matter, as well as further allegations made by Aluko that she had been the victim of bullying and discrimination. However, Aluko has described the inquiries as a “farce”, not least because the FA has admitted the mixed-race player involved in the first allegation was never interviewed. The FA’s explanation was that it did not know her identity even though Aluko’s submission stated it was a mixed-race midfielder – the only one in the squad – during the China Cup in 2015 and even named the player’s club.

The FA has also been heavily criticised after accepting it was aware of the alleged Ebola remark, described as a “racist joke” in a letter from the PFA to the governing body, but choosing not to launch a full investigation on the basis it did not consider it a formal allegation. The same letter from the PFA also alleged that another member of England staff regularly spoke to Aluko in a mock Caribbean accent and the organisation’s chief executive, Gordon Taylor, now believes there should be a second independent inquiry with all the relevant people interviewed.

“The Professional Footballers’ Association has been providing support and assistance to our member, Eniola Aluko, from the first moment she made us aware of her experiences playing for the England team,” Taylor said. “We were naturally shocked and very concerned when we learned of the serious issues Eni had faced and immediately offered her independent legal advice to pursue her complaints together with any other support she felt would be helpful in the circumstances.

“Understandably, we share Eni’s concerns regarding what has occurred and would fully support an open, transparent and independent investigation into her experiences and any other incidents which any of her team-mates may also wish to raise. We feel this is very important to ensure these serious issues are properly dealt with and that an appropriate process is put in place to give any other players the confidence to raise any similar issues.”

Kick It Out has called for the FA to initiate a “comprehensive and independent review of the processes involved” and “take on board any lessons learned, to remedy any deficiencies identified” and “ensure a situation like this will never happen again”.

Aluko, who was born in Nigeria but moved to England at an early age, won the Golden Boot as the leading scorer in the Women’s Super League last season but has not played for England since Dan Ashworth, the FA’s technical director, asked her to participate in a “culture review” because of her status as an “iconic England player”. Aluko, promised it would be a confidential process, raised a number of grievances about Sampson and a week later he visited her at Chelsea’s training ground to inform a player with 102 caps and an 11-year England career she was being dropped for “un-Lioness behaviour”. Sampson and the FA have insisted the two are unrelated and Newton’s report supports that version of events.

Aluko, who was paid £80,000 by the FA after lodging a claim for an employment tribunal, told her side of the story to the Guardian on Monday and a statement from Chelsea said: “We commend Eni for coming forward and speaking about her experiences. Chelsea find all forms of discrimination abhorrent and it is imperative that players are supported when coming forward to speak about these issues.”