CONCACAF's integrity committee released a detailed report on Friday which accused Warner and former general secretary Chuck Blazer of fraud and financial mismanagement.
CONCACAF is the governing body for football in North and Central America and the Caribbean.
As part of its findings, the committee reported that Warner had misused funds provided by Football Federation Australia to support the upgrade of a stadium in Port of Spain, Trinidad.
"The evidence reviewed by the Committee also shows that Warner obtained through fraud and then misappropriated $462,200 provided to CONCACAF by Football Federation Australia in 2010," the report said.
The stadium was part of the Joao Havelange Centre of Excellence in which CONCACAF invested $25.9 million (£17m), which included loans from FIFA, but was found by the report to have been built on lands privately owned by Warner and not by the confederation.
The FFA said they had assisted CONCACAF in their investigation but had only "just been drawn to this area of the report".
"FFA ... looks forward to hearing formally from CONCACAF on its findings and taking the matter from there," the governing body said in a statement.
The FFA said the funding related to "mandatory" World Cup bidding criteria and was intended to demonstrate their credentials in the area of international development.
"This was one of a range of international development projects FFA undertook, which were fully reported to the Australian government as part of its bid reporting processes."
Australia spent more than A$45m (£30m) of taxpayer funds on its ill-fated bid for the 2018 World Cup won by Qatar, splashing large sums on overseas development projects, but was eliminated in the first round after garnering only a single vote from FIFA's executive committee.
David Simmons, a former Barbados chief justice, said the Centre of Excellence was no longer an asset of CONCACAF, but the regional body was looking into legal options.
Warner, who stepped down from his football functions two years ago and is Minister of National Security in the Trinidad and Tobago government, dismissed the report as "baseless" in a statement.