The discovery of Aboriginal human remains on Wadjemup/Rottnest Island last week has been described as "deeply distressing" by Whadjuk Aboriginal Corporation.

Human remains were uncovered during construction works on the island's church grounds last Wednesday, with WA Police confirming on Friday that they were of "Indigenous ancestry."

The remains were found during works to expand the island's main bus stop, with construction at the site now halted.

WAC said the discovery had caused significant distress for Whadjuk Noongar people, given the island's cultural and historical significance.

Wadjemup, about 20 kilometres off the coast of Fremantle, is one of WA's most significant Aboriginal heritage sites and was used as a prison for Aboriginal men and boys between 1838 and 1931.

The Rottnest Island Authority said Aboriginal heritage monitors were present at the time of the discovery, as required during ground-disturbing works on the island.

Monitors are now on site around the clock as authorities determine how to manage the remains.

The discovery has been reported to the Department of Planning, Lands and Heritage in line with the Aboriginal Heritage Act.

The Rottnest Island Authority and Whadjuk Aboriginal Corporation said they are working together to ensure the remains are handled in accordance with cultural protocols.