Northern Territory Police have charged a 21-year-old man with one count of sexual intercourse without consent.
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The alleged assault occurred at the Katherine Hot Springs in the early hours of Saturday.
Police have confirmed the alleged victim was a 21-year-old female.
The incident at the hot springs occurred between 3.30-5.30am on Saturday, police said.
Police were initially searching for two men as a result of the alleged assault.
Police said about 3am on Saturday, the two males are believed to have been in the vicinity of the Katherine Shopping Centre car park.
Katherine detectives made the arrest on Thursday as a result of their enquiries after the alleged assault was reported.
The man was remanded in custody and is scheduled to appear in the Katherine Local Court today.
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