Academy Superintendent Vice Adm. Michael H. Miller said he tossed charges against Midshipman Eric Graham after the judge in the case ruled Graham had not been advised of his legal rights before interrogation, the Washington Post reported Friday.
The judge, Col. Daniel Daugherty, said that failure made Graham's account of what happened inadmissible.
Miller concluded that without Graham's statement, there were "no reasonable grounds" to believe the assault occurred, said academy spokesman Cmdr. John Schofield.
Graham, a senior from Alabama, was one of three Navy students charged with raping a female classmate at an off-campus party in 2012. Miller dropped charges against former Midshipman Tra'ves Bush of South Carolina following a preliminary hearing. Midshipman Joshua Tate, a senior from Tennessee, is due for a court-martial on charges of aggravated assault and making false statements.
The accuser, now a senior, has said she was drinking heavily at the party.
Chip Miller, an attorney for Graham, praised Miller's decision to dismiss charges against his client.
Susan L. Burke, an attorney for the victim, was critical of Miller's action, the New York Times reported. She said there was "substantial other evidence" that could have been used in Graham's trial.
Miller's decision came as the Pentagon released its yearly report on sexual assault and sexual harassment at the U.S. three military academies. Of the 70 cases reported in the previous school year, the report said the most, 45, came from the Air Force Academy. Some 15 cases were reported at the Naval Academy and 10 at West Point.
The Pentagon noted that not all instances of sexual assault and harassment at the academies were reported.
The report said "the same social forces that give cadets and midshipmen a collective sense of identity and purpose at a military academy also work to maintain the silence or complicity of peers when a few misbehave."
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