Mark Sampson, the England women’s team manager, has said he has been through a “difficult and upsetting time” and wants to “move on” from allegations he made racial remarks to two players.

Sampson said his “conscience was clear”, denying both allegations, but said he had regrets over the Eni Aluko case and claimed he was still open to the idea of recalling a player dropped for “un-Lioness behaviour” within two weeks of reporting him to the Football Association.

In his first interview since the allegations surfaced, Sampson insisted Aluko’s 11-year, 102-cap England career had not been ended as retaliation and reiterated that he had been cleared by an internal FA inquiry as well as a separate investigation by the barrister Katharine Newton on behalf of the organisation.

However, his interview leaves the FA facing further questions about its handling of the case following the England midfielder Jill Scott’s comments – “I don’t think we are allowed to answer questions on it” – when the midfielder was this week asked for her views, having been in the meeting at the 2015 China Cup when Sampson, according to Aluko, “distressed” a mixed-race player by asking how many times she had been arrested.

The FA, which denies it has tried to silence the players, refused to let any newspaper journalists attend Sampson’s squad announcement for the game against Russia on 19 September.

Sampson, who insisted he had never thought about resigning, spoke to only two hand-picked media outlets as part of an FA strategy to allow him to make comments in what has been described as a controlled environment.

Asked how hard it had been for him, Sampson said: “It’s been a difficult and upsetting time for everyone involved – myself, my family, Eni, the players and the staff. This has not been a nice situation for anyone but allegations were made, they need to be reacted to, respected, and investigated thoroughly to make sure there are clear conclusions.” Of the allegation that he told Aluko to make sure her Nigerian relatives did not bring the Ebola virus to Wembley, Sampson said: “I’m very disappointed the allegation has come up. I understand it; all I can say is I didn’t say that to Eni.”

Sampson also stated he had received “universal support from the players and the staff” and went on to say he would be willing to meet Aluko and that her England career could “absolutely” be revived.

He added that there was “always going to be an element of regret” but said his only focus was on picking the right players to make England successful. It was not true, he added, that one member of his staff used to talk to Aluko in a mock Caribbean accent.

Aluko has described the two inquiries as a “farce” bearing in mind that the mixed-race player at the centre of one of the allegations was not interviewed for either investigation and that the FA’s review reached its initial verdict before speaking to at least one of the witnesses.

The mixed-race player, who has asked the Guardian not to name her, has provided written evidence to back up Aluko’s story and the Professional Footballers’ Association wrote to the FA last November to complain about “a sham” which was “not designed to establish the truth but intended to protect Mark Sampson”.

The FA maintains there will not be a third inquiry, despite Kick It Out and the PFA saying the case should be re-opened, and Sampson wants to put it all behind him. “These allegations were investigated thoroughly and now we’re in a position where I feel strongly that we need to move on and continue to work hard to bring more success to this team,” he said.