John Allen Wright, 45, was charged with five counts of sexual exploitation of children and one count of possession of child pornography, The (Manchester) New Hampshire Union Leader reported Thursday.
Wright was arrested Sept. 1 on child pornography charges after police discovered during an investigation a hard drive Wright owned that allegedly contained thousands of images and videos.
"Forensic analysis of computers takes a long time," U.S. Attorney John P. Kacavas said. "We're going to be very cautious."
Wright worked for the bus company Provider Enterprises, transporting special-needs students in Rockingham and Strafford counties in New Hampshire when he assaulted two of the male victims.
The third boy named in the case allegedly was assaulted while Wright worked for the Kittery, Maine, school district, transporting disabled students.
Judge Landya B. McCafferty entered an innocent plea on Wright's behalf Wednesday and ordered a psychiatric evaluation after questions were raised about Wright's competency.
A trial date for the case is scheduled for Dec. 14.