The owner of Katherine's main shopping centre plans to charge people $2 to use toilets inside the complex.

The fee would be collected by an attendant and given to a local charity at the Northern Territory town, about 300 kilometres south of Darwin.

Katherine Council chief executive David Laugher says the shopping centre owner wants to keep its facilities clean and improve public safety.

"They experience the same thing that a lot of us experience in the provision of public facilities," he said.

"Bear in mind this is a private facility, not a public one.

"(There is) increasing vandalism, damage and just the general hygiene of the place."

Mayor Fay Miller says she supports the move.

She says people will still be able to use the council's free public toilets away from the shopping centre.

"The toilet facilities within the complex have been abused very badly," she said.

"You would need a cleaner there constantly, and I mean constantly, to ensure they were up to standard."

'Unfair'

However, a Territory Aboriginal legal service says the shopping centre's decision will unfairly target Indigenous people.

North Australian Aboriginal Justice Agency (NAAJA) chief executive Priscilla Collins says Indigenous people are the main users of the facilities.

"When you look at Katherine and you look at the large population of Aboriginal people who are there, and the number of Aboriginal people who go into the shopping centre, it is discriminatory," she said.

"That's really what it's aimed at.

"It is aimed at deterring Aboriginal people from using their toilets.

"Who carries around $2 to go to use the toilet?"

Shopping centre manager Mario Boscaini says the toilet fee is not discriminatory and was put in place after community consultation.

"It is not certainly targeted at anyone in particular," he said.

"All we are saying is that there has been a community concern in regards to the facilities in the shopping centre.

"Looking at another scheme at Alice Plaza in Alice Springs, we thought this was appropriate to introduce."