The suspected remains were found at a building site in the settlement at Rottnest Island, near Perth, authorities confirmed on Friday.
"A ground-penetrating radar survey, anthropological and archaeological work have been conducted at the main bus stop construction site," Rottnest Island Authority said in a statement.
The survey identified 12 potential burial sites at the location, but more archaeological work would be required to confirm this, the authority said.
It follows the discovery of bones at the same construction site on April 8, which were found to be historic in nature and consistent with Aboriginal ancestry.
Rottnest Island Authority said it was working with Whadjuk Aboriginal Corporation to ensure cultural protocols were followed.
The authority will meet with senior Whadjuk Elders and Aboriginal community members on Friday to determine the next steps.
Whadjuk Noongar monitors and will continue to oversee the site as cultural custodians.
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 is famous for its white-sand beaches, shipwrecks and secluded bays where holiday makers sunbake and snorkel.
But the island, which measures 11km long by 4.5km wide, has a tragic past.
WA state records indicate 3700 Aboriginal men and boys were imprisoned there between 1838 and 1931, according to the 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 burial ground lay became a budget camping ground known as Tentland.