The remains were found by workers at Rottnest Island, near Perth, on Wednesday, Western Australian police say.
"The bones, which are believed to be human, were located during construction work on church grounds," a spokeswoman said in a statement.
An investigation has been launched, and forensic specialists will examine the bones to determine their age.
Rottnest, located 19km off the coast from Fremantle, is home to the quokka, a small wallaby-like marsupial, and a popular holiday spot.
Also known as Wadjemup, it has white-sand beaches, shipwrecks and secluded bays where holiday makers sunbake and snorkel.
The island, which measures 11km long by 4.5km wide, also has a dark history.
WA state records indicate 3700 Aboriginal men and boys were imprisoned there between 1838 and 1931, according to the Rottnest Island Authority.
Many were leaders, lore men and warriors, and the removal from their communities had lasting effects.
Living conditions were brutal on the island. Overcrowding and a lack of sanitation and nutrition, extreme weather, and physical and psychological abuse contributed to hundreds of deaths.
Most were buried in unmarked graves on the island.
After the prison closed, one of Australia's largest Aboriginal burial grounds was largely forgotten about, the island authority said.
The island became a holiday resort and the area where the Aboriginal burial ground lay became a budget camping ground known as Tentland.
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