An Aboriginal boy has been detained at an adult inpatient ward for mentally ill people at Royal Darwin Hospital, three weeks after the Territory's first juvenile mental health facility was opened.

The ABC received a complaint about the detention of the boy on Friday from a member of the public.

Earlier this month, the Government said Territory children as young as 12 would no longer be held with adult patients at what is known as the Cowdy Ward.

But the ABC understands the child, under the care of the Children and Families Department, was in the adult ward overnight.

The youth facility is beside the adult unit and has five beds, each in separate bedrooms.

Children and Families Minister John Elferink said the boy was put in the adult ward because at the time of his admission, all the beds in the youth facility were "allocated".

"A decision was then made with the best interest of the child in mind to place the youth in a secure section of the facility," he said.

"The Northern Territory Government takes all appropriate steps for the protection of children in its care.

"There is always extensive case management around every child in the Government's care."