Martin Glenn has denied asking Eniola Aluko to release a statement saying the Football Association is not institutionally racist after the England women's worldwide accused the organisation's chief executive of behaviour "bordering on blackmail".
Senior FA officials later admitted to failings as they came under fire from MPs at a four-hour parliamentary inquiry where they were also accused by experienced global Aluko of having had an "agenda" to protect Sampson and their reputation.
Aluko accused Glenn of "bordering on blackmail" by saying he would only release part of her £80,000 FA settlement if she made the statement, which she "categorically refused to write".
Aluko says the offer was "bordering on blackmail".
"I have re-read and re-considered all the written evidence including all the transcripts of interviews and all the underlying documents, and conclude that my original conclusions on the other individual allegations and also the umbrella allegation of a continuing course of discriminatory, bullying and victimisation should remain untouched".
In his own appearance later, Mr Glenn described how it was the FA's view a Twitter post sent by Ms Aluko broke the terms of the agreement.
Asked whether Aluko will receive the rest of the money owed from the settlement, Glenn replied: "We will reflect on it".
"On behalf of The Football Association I would like to sincerely apologise to Eniola Aluko and Drew Spence".
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"This is not acceptable", he added.
Independent barrister Katharine Newton concluded in her final report - published on Wednesday - that Sampson was not racist, but that he twice made "ill-judged attempts at humour" towards the England pair.
Aluko had claimed that Sampson joked that he hoped that her Nigerian relatives would not bring the dreaded disease Ebola to London on a proposed visit.
At the parliamentary hearing, Glenn, one of four senior FA officials giving evidence, defended the way the FA had gone about resolving the Sampson matter but admitted: "There have clearly been failings".
However, Newton also concluded that Sampson, who was sacked by the FA last month over conduct in a previous role at Bristol Academy, was not a racist and did not subject Aluko to a campaign of bullying.
The 30-year-old, who has been capped 102 times by England but has not made an global appearance since airing her grievances with Sampson, said she felt "vindicated" by the apology.
"Without the PFA support, I wouldn't be sat here and probably wouldn't have got the result I got today", Aluko said. "We regret that the two comments, the inappropriate banter, was made, but the spirit in which we approached the concerns has been good" - Glenn defends the FA's handling of the affair.
"Based on new evidence submitted to independent barrister Katharine Newton, she has now found that they were both subject to discriminatory remarks made by an FA employee".