The teen died early on Monday in the health clinic at Alpurrurulam, west of Mount Isa near the Northern Territory-Queensland border, about 1500km from Darwin.
NT Police said detectives and forensics officers were travelling to the community to investigate the death.
NT Police Acting Commander Mark Grieve told reporters in Darwin the teen suffered cardiac arrest on arrival at the clinic and later died.
"It was at that time that the clinic staff also noticed that she had various number of injuries to her body."
Police believe the girl was transient but primarily resided in Queensland near Mount Isa.
A 26-year-old man believed to have been in a relationship with the girl is in police custody assisting with inquiries.
Alpurrurulam has been the scene of community unrest recently, prompting the evacuation of its health clinic staff.
Acting Commander Grieve said police believed the teen's death was unrelated to the recent unrest.
He said he understood Alpurrurulam community members would like to have a police station, but the viability of doing that was an issue.
13YARN 13 92 76
1800 RESPECT (1800 737 732)
Lifeline 13 11 14
National Sexual Abuse and Redress Support Service 1800 211 028
8°C