The Bureau of Justice Statistics has this report on "Sexual Violence Reported by Correctional Authorities, 2005." The data are compiled pursuant to the Prison Rape Elimination Act of 2003. There were 6241 allegations made to authorities in 2005.
All categories of crime are underreported to some degree, but this one is probably exceptionally so, as the report recognizes: "Administrative records alone cannot provide reliable estimates of sexual violence. Due to fear of reprisal from perpetrators, a code of silence among inmates, personal embarrassment, and lack of trust in staff, victims are often reluctant to report incidents to correctional authorities." BJS is working on a survey method to supplement the reported-to-authorities method. It will be interesting to see how much the two measures diverge.