The 34-year-old man is set to face court after an investigation indicated the teen had died of "blunt force injuries", Northern Territory Police said on Thursday.
"Investigations indicate the man was in a domestic relationship with the deceased at the time of her death," NT Police said in a statement.
Authorities were called to a Galiwinku home, located on an island off Arnhem Land, about 11am on Monday after receiving reports that a 17-year-old girl was unconscious.
"Local police, assisted by staff from the local health clinic, attended the scene, where she was declared deceased," police said.
The 34-year-old was arrested the same day as police launched an investigation at the Elcho Island residence.
Three days later, police charged the man with murder after an autopsy was completed.
Detective Acting Superintendent Paul Lawson described the investigation as "complex".
"Our investigations indicate the deceased has died of blunt force injuries," he said in a statement.
"A young woman has lost her life, and our thoughts are with her family and community."
A file would be prepared for the coroner, he said.
Asked about the pair's relationship, Det Lawson told media in Darwin on Thursday: "The entire circumstances surrounding their relationship, and the goings-on prior to the incident, is going to form part of our brief to the coroner and also the criminal brief.
"The autopsy wasn't conducted until yesterday, and that gave us all the information we needed."
Local officers remained in the community and were working closely with those affected by the tragedy, he said.
"Police would like to thank the community for their assistance during this period.''
The 34-year-old man was remanded in custody and expected to appear in Darwin Local Court on Friday.
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