"The above are merely accusations," a military statement said on Friday. "The accused is presumed innocent until proven guilty and has the right to a fair and impartial trial."
No date has been set for the court-martial.
Japanese police arrested Hadnott in February on suspicion of rape but the case was dropped after the girl withdrew her complaints.
US authorities continued investigating the allegations under the strict military justice code before initiating a court-martial.
Hadnott's arrest and a series of other damaging criminal accusations against US troops have inflamed popular anger at the US military presence on the island.
The rape accusation prompted the US military to severely restrict troop movements on Okinawa and elsewhere, and conduct an ongoing review of its anti-sexual assault education programs and guidelines.
Lieutenant General Edward Rice, the recently-appointed commander of US troops in Japan, demanded high standards of behaviour following the high-profile allegations against US servicemen, including the rapes and murder.
Last month a US sailor was indicted in the stabbing death of a taxi driver near the US naval base in Yokosuka, south of Tokyo.
Four other marines from a base in southwest Japan also face court-martial over the rape of a Japanese woman last year.
About half of the 50,000 US troops hosted by Japan under a security treaty are based on Okinawa, where residents have continuously complained about crime, pollution and crowding associated with the military.