Fairfax Media can reveal that the examination of Football Federation Australia's records is part of a major Swiss criminal probe into an alleged corruption conspiracy said to involve a handful of former European football officials, including German soccer great Franz Beckenbauer.

The FFA, under Mr Lowy's leadership, hired two consultants with close ties to Mr Beckenbauer using part of a $46 million grant from the Rudd government. Swiss authorities have interviewed at least one Australian as part of their investigation. There is no suggestion Mr Lowy or other past or present FFA officials are targets of the Swiss probe.

The revelation of the Swiss authorities' interest in Australian payments comes a day after the release of a sensational FIFA report into the bidding process for the 2018 and 2022 World Cups.

Prepared by FIFA's chief investigator, Michael Garcia, the report is highly critical of the FFA bid team and its consultants. Mr Garcia concluded there was "strong evidence" the FFA made "improper payments" to influence the vote of a key FIFA official.

Mr Garcia also slammed Australia's bid team for trying to conceal its hiring of one of Mr Beckenbauer's closest aides, German Fedor Radmann, as a consultant on a multimillion-dollar taxpayer-funded contract. The FFA also hired another Beckenbauer associate, Andreas Abold, to help with its bid.

While the Garcia report does not accuse Mr Lowy or former FFA chief executive and current North Melbourne Football Club chairman, Ben Buckley, of corruption, it does raise serious questions about their oversight of Australia's taxpayer-funded World Cup bid.

Mr Garcia has included never-before-published emails between key figures in the Australian bid, including lobbyist Peter Hargitay, Mr Lowy and Mr Buckely. The emails reveal what Mr Garcia described as attempts to "mask" the involvement of Mr Beckenbauer's confidant, Mr Radmann, by using codenames to refer to him and his wife's email address to communicate with him.

One telling email from Mr Hargitay to Mr Lowy provides great insight into the circumstances behind the FFA's decision to sue The Age and Fairfax Media over a series of 2010 reports that revealed how much taxpayer money had been promised to consultants like Mr Hargitay and Mr Radmann.

"F just told me about the email Mo got from those mudslingers at The Age. I am OUTRAGED!!!!," Mr Hargitay wrote to Mr Lowy. "It is totally impossible for FFA and you NOT to take legal action ... That nasty piece of work jeopardises everything we have worked so hard for!!!! Franz [Beckenbauer] has now been compromised AGAIN…".

The FFA's legal action never went anywhere and was resolved not long after Australia received just one paltry vote from FIFA's executive committee for its 2022 World Cup bid. But it made Fairfax Media nervous about continuing to report on the World Cup bid and had the effect of deterring other media interest.

Mr Garcia's report was also critical of the FFA's plan to use Australian government aid money in Africa to target four African countries represented on FIFA's executive committee.

"FFA's approach to funding development projects in Africa and elsewhere is a further unfortunate example of bid teams using money that should be awarded based on humanitarian considerations to curry favour with officials eligible to vote on December 2, 2010," Mr Garcia concluded.

In a statement released on Wednesday, the FFA said it was thanked by Mr Garcia for providing "full and valuable co-operation" to the inquiry.

The FFA said the Garcia report did not raise "substantive new matters" that had not already been previously covered.

"FFA reiterates that the financial management of the bid was routinely reported to government and reviewed by independent external auditors … FFA has said repeatedly that the bid process for 2018 and 2022 was deeply flawed and that mistakes were made by the Australian bid team."

A $500,000 payment by the FFA to a Caribbean bank account linked to former FIFA vice-president Jack Warner has also been investigated by the Australian Federal Police.

AFP correspondence from March this year reveals its officers claimed to have conducted a "thorough" inquiry into the payment to Mr Warner, who is accused of stealing the money rather than using it for the benefit of Caribbean soccer. The AFP concluded it could not identify any Commonwealth offences in relation to the payment.

But Mr Garcia described the same payment as "significant evidence that the AU$500,000 was paid with the intention of influencing Mr Warner's World Cup vote."

While the Garcia report paints an abysmal picture of the FFA World Cup bid's governance and practices, it does not provide any prima facie evidence that $14 million in consulting payments the FFA made to Mr Radmann and Mr Abold were ever passed to any third party. Mr Radmann and Mr Abold have denied making any such payments.

Veteran SBS soccer commentator Les Murray is also mentioned in the Garcia report due to his relationship with Mr Hargitay and role on FIFA's ethics committee.

The report reveals how Mr Murray in January 2009 forwarded an email to Mr Hargitay which he had earlier sent to the chair of FIFA's ethics committee, former English Olympian Sebastian Coe, in which the Australian commentator asked to discuss a potential investigation into conduct by the English bid team.

After receiving the email from Mr Murray, Mr Hargitay forwarded it to Mr Lowy, with the added comment: "Boom. Here we go :):)." A month later, Mr Hargitay urged FFA chief executive Ben Buckley to make Mr Murray a "bid ambassador" for Australian despite his position on FIFA's ethics committee.

The on-going Swiss investigation, which is separate from the completed Garcia probe and whose interest in the Australian bid has not before been made public, has far greater investigatory powers than those available to Mr Garcia.

Last September, the Swiss Attorney-General's office confirmed that Mr Beckenbauer was under investigation for fraud and other offences related to Germany's bid to host the 2006 World Cup but released no further details.

In other potentially worrying news for the FFA, the US Justice Department is continuing to investigate alleged corruption within FIFA. The US investigation is understood to have examined the $500,000 payment by the FFA to the Caribbean bank account linked to Mr Warner on the basis the transaction involved part of the American banking system.