Police have charged a man with murder in relation to the death of a 16-year-old girl in the remote Northern Territory community of Alpurrurulam.

At 5.30 am on Monday, police received a report from the local clinic — close to the Queensland border and 1,200 km from Darwin — that a teenage girl had died after allegedly being physically assaulted.

The 16-year-old presented herself at the clinic, where she suffered a cardiac arrest and later died.

"It was at that time that the clinic staff also noticed that she had a number of injuries to her body," NT Police Acting Commander Mark Grieve told reporters on Monday.

Late on Wednesday evening, NT Police charged a 26-year-old man, who was believed to have been in a domestic relationship with the teenager, with murder.

The man had previously been arrested and taken to Darwin. He was remanded to appear in Darwin Local Court on Thursday.

Acting Commander Grieve said police believed the teenage girl was from Mount Isa but that she was "quite transient between here and there".

Local police, with assistance from Avon Downs police, responded to the death, while detectives from Crime Command and forensic officers travelled to the community from across the NT.

There has been no permanent police station in Alpurrurulam since 2018, while the local health clinic was evacuated following unrest in the town.

However, the clinic was staffed when the teenage girl arrived, as health personnel had returned to the community.

The closest police officers are stationed in Avon Downs, 170 km away.

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