Australia's largest hotel chain have allegedly been giving Aboriginal customers the worst rooms in one of their hotels and charging them the same as other guests.

An investigation by the ABC's Background Briefing uncovered an email allegedly telling staff to racially discriminate at the Ibis Styles hotel in Alice Springs.

In the email allegedly sent to staff at the hotel, which is part of the French transnational operator Accor, employees were allegedly told to put Indigenous guests into hospital linen-only rooms.

Australia's largest hotel chain have been allegedly caught giving Aboriginal customers the worst rooms in one of their hotels even though they are charged the same as other guests (hotel pictured in Alice Springs)

'Just to keep everyone in the loop we are now only putting hospital linen into rooms 85 to 90,' the directive said.

'These are to be referred to as community rooms and we will try to limit them to just that.'

The term 'communities' is used in Alice Springs to describe Aboriginal people who have come from out of town.

A staff member, who blew the whistle on the alleged practices at the Alice Springs hotel, said they had seen guests being segregated along racial lines hundreds of times.

The hotel chain said it had taken immediate action over the allegations - which included ordering 'cultural training' for its employees.

'An internal investigator has been appointed and we will appoint an external investigator to advise on this review,' a spokesperson said.

'At this time, interim management has been appointed to the hotel while we investigate.

'Local anti-discrimination training next week with every team member at the hotel will reinforce our ongoing expectation to treat others with dignity and respect and so every guest is made to feel welcome.'

An investigation uncovered an email allegedly telling staff to racially discriminate at the Ibis Styles hotel in Alice Springs (stock image)

Two groups of guests - one comprised of Aboriginal people and another of non-Indigenous people - were sent by the ABC to stay at the hotel.

It is alleged they confirmed the whistleblower's report that Indigenous people received inferior rooms.

Stained sheets, clothes belonging to previous occupants, exposed wiring and a stale smell were all allegedly present inside room 86.

In a statement, Accor said it had taken action over the allegations - which included ordering 'cultural training' for its employees

By contrast, the non-Indigenous group claimed they were not plagued by any of the same problems even though they paid the same $129 room rate.

Speaking to The Guardian, an Alice Springs resident said she too believed she had experienced racial segregation at the hotel.

'As soon as we entered the room you could physically see the dirt,' she claimed.

Aboriginal justice lawyer Sophie Trevitt said the practice of separating Aboriginal guests was happening across the Northern Territory.

'It's effectively a form of segregation within hotels and hostels,' she said.