England coach Sven Goran-Eriksson told FA bosses he never had an affair with sex scandal PA Faria Alam, an employment tribunal has heard.
Faria Alam is thought to be seeking £30,000 in compensation
Executive director David Davies said the Swede had seemed "taken aback" when asked about his relations with Ms Alam.
Mr Davies, 57, also hit back at "deeply hurtful" claims by Ms Alam, 39, that he had sexually harassed her.
Ms Alam resigned after it emerged she had had affairs with both Mr Eriksson and chief executive Mark Palios.
Ms Alam, who was Mr Davies' personal assistant, is claiming unfair dismissal, sexual discrimination and breach of contract against the FA and is thought to be seeking £30,000 in compensation.
She denies quitting her job so as to make money from newspapers.
Giving evidence at the central London tribunal, Mr Davies said he telephoned 56-year-old Mr Eriksson on 17 July 2004 after the News of the World newspaper warned the FA it was about to print a story about his affair with Ms Alam.
He said: "I can say that I believed quite clearly at the end of that conversation that he was not having an affair with my personal assistant.
"He seemed quite taken aback by my direct question."
He added: "I spoke to both Sven and Faria, both of whom denied that there was any truth in the story."
Sven Goran-Eriksson was ruled to have "no case to answer" by the FA
He said Ms Alam later admitted she had misled FA officials.
Mr Eriksson - who will lead England's 2006 World Cup campaign - was allowed to keep his high profile job after an internal FA inquiry ruled he had never lied and had "no case to answer".
The FA made a public statement on 25 July admitting the affair had taken place.
Under cross-examination, Mr Davies reiterated that he had believed there had been no affair, but declined to confirm exactly what Mr Eriksson had said during their conversation.
"Half-truths and fantasy"
He denied suffering from "selective memory" but confirmed he and his wife were close friends of Mr Eriksson and his partner, Nancy Dell 'Olio.
He said that in the 72 hours after newspaper stories about the relationship broke, he considered it his duty to protect his friends.
When pressed to say whether Mr Eriksson had lied to him about the affair, Mr Davies said that was a question which would have to be put to the England manager himself.
Mr Davies dismissed his former PA's claim that he sexually harassed her and made a string of "unwanted advances" as "a mixture of half-truths and fantasy".
He told the hearing he had been flabbergasted at the betrayal by "a trusted friend".
He told the hearing: "Faria's allegations are deeply hurtful and upsetting, I have reacted to them with sadness and incredulity."
"I trust she understands the impact of them on my life and the lives of those around me," he added.
The hearing continues.