The women had been expected to support Ms Alam's allegation that she suffered persistent sexual harassment from David Davies, a former BBC sports presenter who is the executive director of English football's governing body.
Instead, an employment tribunal in central London was told yesterday that Kim Fisher and Sarah Ford, who are no longer employed by the FA, had been tracked down at the last minute by lawyers for the organisation and sided with Mr Davies.
The development came after Ms Alam, 39, this week named Mr Davies as the "third man" in a sex scandal at the FA including her relationships with the then chief executive, Mark Palios, and the England manager, Sven Goran Eriksson.
The secretary, who only added details of the allegations against Mr Davies to her case last week, had not produced statements from the two women. She said that the pair had taken her aside when she arrived at the FA in July 2003 and warned her that her boss "had a bit of reputation".
But in an unexpected twist to proceedings, Jeffrey Bacon, for the FA, revealed that his team had tracked down the two women – one of whom now lives in south-east Asia – earlier this week and obtained testimony rubbishing Ms Alam's claims.
Mr Bacon said: "They were so indignant that they gave witness statements, they absolutely refuted what you said."
In her statement, Miss Fisher said: "In my five years at the FA, I had no complaint with David Davies in that respect. I never felt uncomfortable with him and he never tried it on with me."
Miss Ford, who worked in the operations department of the FA, further denied telling Ms Alam that the organisation's computer experts had hacked into her private e-mail account once her affair with Mr Eriksson became public after the Euro 2004 tournament. She added: "I never told Faria that David tried it on with me. I would describe our relationship as businesslike rather than social."
Ms Alam, looking tired after two days of cross-examination, insisted that the warning had been given "behind closed doors" by the two women. She said: "We all knew nothing would come of this, we couldn't say." The tribunal heard a claim that the secretary had also left out crucial information when she alleged that Mr Davies complained she had not sat next to him at an FA Christmas party.
Mr Bacon said: "Mr Davies in fact saw you sitting between Mr Palios and Mr Eriksson and you were playing footsie with Mr Palios under the table."
In bad-tempered exchanges, the former personal assistant rejected Mr Bacon's accusation that she had embellished her claims against Mr Davies last week to push the FA to settle the case. Ms Alam, who is claiming sex discrimination and unfair dismissal against the FA, said: "This is nothing to do with money. The FA is completely male-dominated. I am just a mere woman, so what do I really matter? Why would my complaints be taken seriously?"
Later, the FA's former director of communications, Colin Gibson, admitted he had tried to strike a deal with the News of the World to reveal details of the relationship between Ms Alam and Mr Eriksson in order to protect Mr Palios, who was at the time attempting a reconciliation with the mother of one of his five daughters.
Mr Gibson, who resigned after the newspaper revealed his proposal, said the FA had been placed in an impossible position by accepting Ms Alam's initial denial of any sexual relationship with Mr Eriksson.
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