Australia voted last year for Prince Ali when he stood against incumbent Sepp Blatter, who has since been banned for six years for ethics violations.
"Under all the circumstances FFA believes there is merit in continuing to support Prince Ali on this occasion," Football Federation Australia (FFA) chairman Steven Lowy said in a statement.
"Prince Ali is a long-standing and consistent advocate for reform at FIFA and his manifesto spells out a clear vision of the way forward."
World football was plunged into crisis last year after several dozen officials were indicted for corruption in the United States and a criminal investigation was begun in Switzerland.
Prince Ali is one of five candidates standing to replace Blatter to try to lead FIFA out of its crisis.
Gianni Infantino, the Swiss general secretary of European governing body UEFA, and Asian football boss Sheikh Salman bin Ebrahim Al Khalifa of Bahrain are seen as the favourites to beat in the vote on Friday.
South African businessman Tokyo Sexwale and former French diplomat Jerome Champagne are the other candidates.
The FFA said it would also vote in favour of each proposal in the package of governance reforms at Friday's congress.
The reforms, which include the introduction of term limits for top officials and disclosure of earnings, are seen as vital in cleaning up the beleaguered global football governing body.
"In addition to reforms on term limits and better governance, we are especially proud to support the reforms on gender equality," Lowy said.
"It is critical that the reforms are implemented with conviction and that they signal a new beginning for FIFA."
(Reporting by Ian Ransom; Editing by Greg Stutchbury)
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