Pena, 28, was arrested Monday. When a 19-year-old woman enlistee sought his guidance, he advised her how to leave the military, got drunk with her and her cousin and sexually assaulted her, the arrest warrant affidavit states.
Pena could face additional charges, Alamo Heights police Sgt. Tom Vitacco said Tuesday.
The U.S. Navy is cooperating with police since it learned of the allegations, Navy spokesman Jeffrey G. Nichols said in an email.
"The sailor has been removed from all recruiting duties pending further investigation," Nichols said, adding the Navy would consider disciplinary action after the civilian criminal case ends.
Pena's arrest comes amid increased scrutiny of sexual misconduct in the military, focused in the past year on nearby Joint Base San Antonio-Lackland Air Force Base, where 32 instructors have been implicated in a scandal involving 62 recruits and students, the San Antonio Express-News reported Wednesday.