"These charges are accusations, and Midshipman Owens is presumed innocent until proven otherwise," academy spokesman Cmdr. Rod Gibbons said.
Since the alleged attack last month occurred on academy grounds, Owens was charged under the Uniform Code of Military Justice, and the investigation is being handled by the Naval Criminal Investigation Service, Gibbons said.
The academy did not release the name of the woman. Gibbons said the academy was offering her support and counseling.
Owens, a 22-year-old senior from Savannah, Ga., would not be available to comment, Gibbons said.
"He remains assigned to the Naval Academy and will continue to attend class, performing other duties normally assigned to midshipmen pending results of the investigation," Gibbons said. He said the academy took steps to prevent contact between Owens and the woman.
An Article 32 hearing, similar to a civilian grand jury inquiry, will be held to determine if there is sufficient evidence to go ahead with the case, Gibbons said.
The military academies have been under scrutiny since 2003, when women at the Air Force Academy in Colorado began coming forward with accusations that they had been sexually assaulted by fellow cadets over the previous decade and were ignored or ostracized by commanders when they spoke out.
A Pentagon task force found that hostile attitudes and inappropriate treatment of women also persisted at the U.S. Military Academy at West Point and at the Naval Academy.
Earlier this month, a senior at the Coast Guard Academy in New London, Conn., was charged with sexually assaulting six female cadets in the campus barracks and other sites. Webster M. Smith, 22, a linebacker on the academy's football team, was charged under military law with rape, assault, indecent assault and sodomy, school officials said. Smith insists he is innocent, his lawyer has said.
Owens guided Navy's football team to an 8-4 season record that included victories over Air Force and Army and a victory in the Poinsettia Bowl over Colorado State.
Scott Strasemeier, head of the Navy's sports information office, said Owens' athletic eligibility is complete. He declined to comment on the allegations. The academy's 2006 starting quarterback will be chosen during spring practice, which starts March 27, he said.