The tech giant "made false, misleading, or deceptive representations about consumers' rights under the Australian Consumer Law," the Australian Competition and Consumer Commission (ACCC) charged.
The proceedings, against Apple Pty Limited and its US-based parent Apple Inc, were brought on behalf of 275 consumers.
Under Australian law, each breach can attract a fine of up to Aus$1.1 million (US$830 million), although it is up to the court to determine the size of the penalty.
These customers previously had their devices serviced by a third-party, "even where that repair was unrelated to the fault", the government body said.
"Consumer guarantee rights under the Australian Consumer Law exist independently of any manufacturer's warranty and are not extinguished simply because a consumer has goods repaired by a third party," ACCC chairman Rod Sims said in a statement.
"Denying a consumer their consumer guarantee rights simply because they had chosen a third-party repairer not only impacts those consumers.
Apple in Australia had no immediate response. Sims said companies must remember that consumer rights extended to software or software updates on goods they sell.
"Faults with software or software updates may entitle consumers to a free remedy under the Australian Consumer Law," he said, adding that the ACCC was seeking remedies including financial penalties.
It is not the first time Apple has fallen foul of the ACCC.
In 2013, it worked with the watchdog over a court-enforceable undertaking after alleged "misleading representations" to customers that it did not need to refund, replace or repair some products even though required to under Australian law.
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