Arapahoe County District Judge William Sylvester rejected the request Thursday, The Denver Post reported.
Prosecutors argued that those shot and wounded during a July 20 midnight showing of the movie at a theater in Aurora might be harassed or intimidated if their names were available to the public but Sylvester said removing the names now would have little practical effect.
James Holmes, a former University of Colorado graduate student, has been charged with killing 12 people and wounding 58.
Sylvester said he would have some information restored to the files. The Post and other news organizations, in addition to opposing the prosecutor's request on the names, argued the court had gone too far in removing information that might be prejudicial to Holmes.
"Despite the unusual and relentless media attention in this case, the investigation and proceedings in this case should, whenever possible, conform to the rules and usual practices of any other criminal case in Colorado," Sylvester wrote in his opinion.