Tax commissioner Chris Jordan has taken issue with some of the things multinational companies told a recent hearing into corporate tax avoidance.
Mr Jordan appeared before the Senate inquiry in Sydney on Wednesday and was asked whether tech giants Google, Apple and Microsoft had misled senators over their tax arrangements.
"Mislead is a subjective term, but we do take issue and dispute some of the comments that have been made," the commissioner said.
The Australian Taxation Office is contesting Apple's statement that all revenue from its Australian sales is recognised for tax purposes. Some profits are transferred to low-tax jurisdictions.
In the case of Microsoft, Mr Jordan said the ATO was trying to determine whether its statement that profits from Australian business are primarily earned in Singapore - around $2 billion, with $100 million remaining in Australia - was the appropriate split of revenue.
"We further understand that much of this Singapore profit paid out as technology fees ends up in Microsoft Bermuda," he said.
The commissioner also questioned Google's statement that Australian revenue from advertising was booked and taxed in Singapore.
The ATO believes the majority of profits made in Australia end up in Bermuda where no tax is paid.
The ATO is also "robustly testing" miner Rio Tinto's claim that profits in a Singapore hub was the result of "arms-length transactions".
Additionally, while fellow miner BHP Billiton confirmed it was in the early stages of an audit of its Singapore hub, Mr Jordan said the company was disputing millions of dollars from previous Singapore hub activity.
Mr Jordan said the ATO did not accept the statements at face value.
"This is the point of the audits we are undertaking to determine whether aggressive tax planning is taking place," he said.
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