In 1997, Horiuchi was charged in Boundary County, Idaho state court with involuntary manslaughter. Horiuchi successfully petitioned to remove the case to federal court, where the case was dismissed by U.S. District Judge Edward Lodge on May 14, 1998, who cited the supremacy clause of the Constitution which grants immunity to federal officers acting in the scope of their employment. This decision was reversed by an en banc panel of the Ninth Circuit, which held that Horiuchi should stand trial. However, shortly after the Circuit court rendered its decision, the prosecutor moved to drop the case, and the District court granted the motion on June 26, 2001.
Horiuchi remained employed with the FBI throughout his prosecution.