The man, aged in his 20s, was found unconscious in his cabin on Navy patrol boat at 5am, by a fellow sailor, and could not be revived.
The ship was docked at Darwin's Larrakeyah naval base.
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The family of the sailor, who has not been named, have been informed of his death.
Police are investigating the case, and say the man had no immediately visible injuries, and his death does not appear to be suspicious.
An autopsy will be conducted on the body tomorrow.
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