Aboriginal guests at the Ibis Styles hotel in Alice Springs were purposely put in inferior rooms after a directive last June, the ABC reported on Friday.
They were charged the same price as guests placed in better rooms.
Accor said the alleged practice went “completely against” its values.
“[We] were made aware of the matter… and are taking prompt and decisive action on this incident at the highest level,” the hotel group said in a statement to the BBC.
“We are extremely saddened and disappointed as it completely goes against our values,” it added, saying it had a long track record of engaging with Australia’s indigenous community.
Paris-based Accor is one of the world’s largest hotel groups, with properties in more than 100 countries.
‘Please allocate accordingly’
Employees at the Ibis Styles Alice Spring Oasis – located in the southern desert region of the Northern Territory – were sent an email last June instructing them to direct Aboriginal guests into one of six designated rooms, the ABC reported.
One whistleblower who spoke to the national broadcaster’s Background Briefing programme said this had happened “hundreds” of times, adding that it was “pretty much standard”.
“We are now only putting hospital linen into rooms 85 to 90… these rooms are to be referred to as community rooms and we will try to limit them to just that, those coming from the communities [a local term for aboriginals from outside the town],” the email reportedly said.
It also asked those working at reception to “please use a touch of initiative and allocate accordingly”.
The ABC sent two groups of people to the hotel as part of its investigation – the group that was made up of indigenous Australians was sent to the “community rooms”.
Both the non-indigenous and indigenous groups were charged A$129 (£60; $90).
The ABC found stained sheets and towels, broken glass and rubbish in the patio area of room 86. One indigenous guest found chicken bones inside the bathroom.
Indigenous Affairs Minister Nigel Scullion called the incident “very concerning”, saying it would be looked into.
Accor told the BBC that it “prided itself on being an inclusive organisation”, saying it had “strict anti-discrimination policies in place” and was proud of its relationship with the indigenous community and its indigenous employees.
It said it was moving to reiterate “the non-negotiable values of our business and specifically undertake cultural training at the hotel immediately”.
The recognition and treatment of indigenous Australians remains highly controversial.
Aboriginal or Torres Strait Islander people make up about a quarter of the population of the Northern Territory, according to the 2016 census.