Benjamin Batchler had been on the run since police issued a warrant for his arrest on October 3.

Batchler has been charged with two counts of sexual intercourse gross indecency and one count of aggravated assault.

On October 11, police swarmed on the Katherine Hot Springs - a popular tourist attraction - and closed the nearby Low Level bridge after a reported sighting of Batchler.

While police would not confirm how many officers were involved in the operation, Commander Bruce Porter said at the time members of the public had been turned away from the area for their own safety.

"The operation undertaken at the Hot Springs and Low Level crossing over the weekend was to follow-up on reports of a possible sighting of Mr Batchler in that area," he told the Katherine Times on October 13. 

"Police believe he is actively avoiding any contact with our officers.

"In light of this, members of the public were turned away at the Hot Springs and the Low Level for their own safety."

Following his apprehension last  night, Superintendent Sachin Sharma praised the community for its continuous support over the past 12 days.

"It is good see our tightly-knit community coming together and assisting police," he said.

"Their patience during recent operations in the town of Katherine is appreciated."

Batchler will appear in Darwin Magistrates Court today.