The school confirmed the allegations, but would not describe the attacks, citing a policy of not discussing cases under investigation.
But the senior's lawyer said Thursday that the school charged his client with raping the female plebe in his dormitory room in November and assaulting her in March during an attempted rape in a school bathroom.
Robert A. Curcio, 23, of Antioch, Calif., denies the allegations, said his lawyer, Greg D. McCormack. "Our position is that the allegations are flagrantly false, that we have evidence that she has made significantly contradictory statements," McCormack said.
He said the Navy has held an Article 32 hearing, similar to a grand jury inquiry, on the charges and that a decision is likely within a week or two.
While an investigating officer weighs whether enough evidence exists for a court-martial, Curcio is taking two classes at the school this summer to earn enough credits to graduate. The woman has resigned from the academy.
The Naval Criminal Investigative Service began an investigation of Curcio in November after the woman complained he had lured her to his dorm room with an offer of strawberries and raped her.
School officials ordered Curcio to have no contact with the woman and sent him to live at Naval Station Annapolis, just across the Severn River, while he continued to take classes at the school.
But he was then accused of trying to sexually assault the plebe March 29 in a basement bathroom in the Bancroft Hall dormitory after she returned from a late-night jog.
McCormack said the woman said Curcio gagged her, covered her eyes with a blindfold and scratched her on her hands and thighs. "The March 29 incident is the key in this case because we have an ironclad alibi that he was not in any manner in that area," McCormack said.
Because the alleged offenses took place on academy grounds, they are being handled through the military justice system.
In addition to the rape and attempted rape counts, Curcio is charged, among other things, with sexual harassment, violating a protective order, conduct unbecoming an officer and a gentleman and having consensual oral sex with the woman in his dorm room in October, a violation of a rule barring sex in the dorm.
"When these allegations were brought to our attention, we investigated promptly and thoroughly," said Cmdr. Rod Gibbons, an academy spokesman. "The academy has several tools to protect both the victim and the accused."
Asked why Curcio was allowed to continue taking classes even after the woman complained in March of the second assault, Gibbons said, "while we investigate, both the accused and the victim have rights that are protected."
"The accused is presumed innocent until other information shows otherwise," he said.
Last week, the woman, who is from Virginia, testified for more than six hours during the Article 32 hearing.
The plebe testified she and Curcio, members of the same company in the brigade, met early in her plebe year, according to the Navy Times, which first reported the story.
McCormack said there was minimal contact between his client and the woman, but that "the relationship never got to be a personal relationship."
"He denies having any improper relationship with her," McCormack said.
Gibbons said the case remains under investigation.