It claimed an estimated Aus$8.9 billion in untaxed profits from Australia had been moved to a tax haven structure in Ireland, paying just 0.7% of its turnover in tax.
Last year, Apple reported pre-tax earnings in Australia of only Aus$88.5 million after sending an estimated Aus$2 billion from its Australian sales to Ireland via Singapore, it reported.
Apple in Australia declined to comment to AFP, but it has previously said it has complied with the law and done everything required by the tax office.
The report follows last month's G20 finance ministers meeting in Sydney that agreed to new measures to crack down on international tax evasion, including the automatic exchange of information between member nations.
It came as concern mounts that companies, particularly those involved in the digital and Internet sectors, can reduce their tax bills by shifting profits around the world to areas where rates are lowest
Ahead of the meeting, IMF chief Christine Lagarde said accounting for revenues from global digitised businesses like Apple and Google was a "big ongoing problem and process".
She urged governments to radically rethink international tax arrangements to deal with it.
The Organisation for Economic Cooperation and Development (OECD) is expected to present a report looking at the increasingly digitalised global environment to another G20 meeting in Cairns, in northern Australia, in September.