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Emergency services launched a search and rescue operation near Lake Mackenzie on World Heritage-listed Fraser Island off the Queensland state coast late on Friday after the boys were reported missing.
Police located the bodies in the water early on Saturday morning.
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"This is a tragic event, there is no doubt about that," police inspector Tony Clowes told reporters Saturday.
Clowes said there was nothing to immediately indicate suspicious circumstances surrounding the drowning, but said more would be known as they prepare a coroners report.
The public need to be aware of their swimming abilities before entering Australian waters, Clowes added.
"Be aware that if you are entering water there is some inherent risk with entering waterways in this country," he said
Clowes said families of the boys have been notified and authorities were working with the Japanese consulate to provide support.
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Fraser, the world's largest sand island, is popular with tourists for its beaches - and is also well-known for its dingoes.
Two of the wild animals were put down earlier this month after a French mother and son were mauled by dingoes on the island.
It followed an attack in January when a six-year-old boy was mauled by the native animal after as he ran up a dune on the island.
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