The suspects' names were not made public by academy officials, The Washington Post reported. Their names won't be released officially until a preliminary hearing expected to take place this summer, military law experts told the newspaper.
The female midshipman's attorney said her client, now 20, was reprimanded for drinking.
The sexual assault is alleged to have occurred at an April 2012 party at an off-campus house used by Navy football players.
Naval Academy Superintendent Vice Adm. Michael H. Miller decided the case should proceed to an Article 32 hearing based on investigators' findings, academy spokesman John Schofield said. That hearing will determine whether the case should proceed to a court-martial.
"This case is still in the pre-trial phase, so any further comment on this ongoing investigation would be inappropriate," he said in a written statement.
The Post said the female midshipman has said previously she drank heavily at the party and woke the next morning with bruises, but no memory of being raped. She told CBS News Monday she began hearing of the alleged sexual assault through posts on Facebook and Twitter. She said there were witnesses and the three accused midshipmen, one of whom was to graduate this May, had bragged about what they did.
The athletes were allowed to keep playing despite the investigation, her attorney said.