Ryuki Takamine of the Okinawa Prefectural Police Department told ABC News the department received a report by the victim and is looking into the matter.
"No arrest has been made but we have been talking to the victim," Takamine said. The victim remains hospitalized and Takamine refused to elaborate on the nature of the injury or the condition of the victim.
Master Sgt. Terence R. Peck of the U.S. Forces Japan Public Affairs Office said the U.S. military is "aware of the allegation and is taking it very seriously."
Amid severe criticism from Japanese, the U.S. military started to restrict its personnel in Okinawa to bases, workplaces or off-base homes except for work, worship, school or medical appointments.
The order, "a period of reflection" that took effect Wednesday, is said to be in place indefinitely.
Today, U.S. bases across Japan observed a "Day of Reflection," where military personnel attended lectures and held discussions on issues such as professionalism, core military values, sexual harassment and sexual assaults.
"I did not feel anything special or reflective about today," said Tetsuei Tamayose, a 73-year-old Okinawan who lives in Naha City. "You cannot just wing something like that in a hurry. It does not mean anything."
Tamayose was one of the organizers of a rally in 1995, when three U.S. servicemen kidnapped and raped a 12-year-old Japanese girl in Okinawa.
"Boy, did I get a flashback of that time," said Tamayose, the head of Okinawa Prefectural Liaison Council for Development of Kodomo-kai (children's association). "I certainly did not expect something as horrible as that to happen again in our community. What are they thinking?"
Local organizations have held several protests outside the U.S. bases in Okinawa.
Hideaki Okuno of the Okinawa Prefectural Assembly said his office has been hearing from different groups wanting to organize another big rally.
"About 85,000 people showed up at the rally in 1995," said Okuno. "We are not certain whether there will be a rally at this point, but locals are talking about the possibility of one."
Tamayose said children in his neighborhood are fearful of U.S. servicemen.
"I have spoken to some junior high school girls. They said they do not want to walk near the military people anymore," Tamayose said. "I heard the suspect said he did not know the girl was a junior high school student. Does that mean if the girl was of an adult age, his conduct somehow could have been justified? As far as I know, the presence of the U.S. military has never brought peace to Okinawa. So long as we have their presence, there is always a dark cloud over our heads."