An application to have the case against a US Navy sailor charged with rape in Darwin heard outside Australia has been rejected.

The 22-year-old sailor is charged with sexual intercourse without consent, the deprivation of liberty and aggravated assault over the alleged rape in September.

He was arrested by Northern Territory police while assigned to the USS Denver, which docked in Darwin.

Earlier this month, the Darwin Magistrates Court heard the US embassy had applied to the Commonwealth's Attorney General to have the matter removed from the Northern Territory's jurisdiction and handled by the US Navy.

That application was refused.

The prosecution said it was applying to obtain critical Facebook material relating to the case.

The accused sailor has been released on bail and has rejoined his unit in Japan.

He will return to Australia when he is due to appear for his preliminary court hearing in the Darwin Magistrates Court in early January.

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