Football Federation Australia demanded answers after a $462,000 donation it made to a Caribbean soccer organisation was allegedly stolen by disgraced former FIFA kingpin Jack Warner.
The incident was detailed in a damning integrity report by the Caribbean, North and Central American international football body, CONCACAF, that accuses Warner of enriching himself through fraud.
The report compiled by several former judges into the financial management of CONCACAF relates to when Warner, a former vice-president of FIFA who quit in 2011 after being accused of paying bribes, headed the organisation.
It said FFA paid a cheque into a Caribbean bank account maintained by CONCACAF in 2010 to help the Trinidad and Tobago Football Federation improve a centre of excellence (COE).
The donation was part of Australia's attempt to demonstrate its international football credentials during its failed bid to host the 2022 World Cup.
But the account was allegedly controlled by Warner, who pocketed the money and never declared it to CONCACAF, the report said.
"The committee concluded that Warner committed fraud and misappropriated funds that were sent by Football Federation Australia to CONCACAF for development of the COE," the integrity report said.
"(He) breached his fiduciary duties to CONCACAF through fraud and misappropriation of funds."
Warner, who stepped down as CONCACAF president in 2011, denies any wrongdoing but resigned as Trinidad and Tobago's minister of security over the weekend.
Media in Australia said the donation raised questions about the FFA's decision to give lucrative grants to football organisations headed by influential FIFA officials previously accused of corruption.
But an FFA spokesman told AFP the cash was donated with "complete transparency" and Australian football authorities only became aware it had allegedly been misused when the CONCACAF report came out on Friday.
"FFA is currently considering the findings of the CONCACAF Integrity Committee report," said the FFA's chief spokesman.
"FFA has assisted CONCACAF in this investigation and yesterday wrote to CONCACAF regarding next steps."
He said the funding "related to the mandatory FIFA World Cup bidding criteria".
"FFA was required to demonstrate its credentials in the area of international development," he said, adding that all funding was reported to the Australian government.
Despite a $45 million grant from the government and intense lobbying, Australia managed to secure just one vote when the FIFA executive committee decided the the 2022 hosts.
Qatar was controversially awarded the hosting rights.