The Australian Defence Department has confirmed a US sailor has been arrested and charged in relation to an alleged rape in Darwin in September.

The 22-year-old has been charged with sexual intercourse without consent, the deprivation of liberty and aggravated assault.

He has been released on bail and is due to appear again in court in January.

Defence says the matter is being managed in accordance with Northern Territory and Australian law, and with an agreement between Australia and the US.