In May 2005, Pappas was disciplined by the Army for failing to properly supervise and train subordinates and for allowing military dogs to be present during prisoner interrogations.
Fay also found that Pappas showed poor judgment by leaving Lieutenant Colonel Steven L. Jordan in charge of the JIDC during critical stages and improperly authorized the use of dogs during interrogations, failed to take action regarding International Committee of the Red Cross reports of abuse, failed to take aggressive action against soldiers who violated procedures and the Geneva Conventions, failed to report that his unit would be unable to accomplish its mission due to lack of manpower and resources and allowed his subordinates to be subjected to inordinate pressures from higher headquarters, and failed to establish appropriate coordination between military intelligence and military police which would have alleviated confusion surrounding the abusive environment at the prison.
In May 2005, Pappas received non-judicial punishment for two counts of dereliction of duty under the Uniform Code of Military Justice for failing to ensure that subordinates were adequately trained and supervised in application of interrogation procedures and for failing to obtain approval of superiors before authorizing the presence of military working dogs during prisoner interrogations.
[1] In November 2006, human rights attorney Wolfgang Kaleck filed a high-profile criminal complaint at the German Public Prosecutor General against Donald Rumsfeld and several other US officials and officers including Thomas Pappas for their alleged involvement in human rights violations at the Abu Ghraib prison.
[6] In August 2007, Pappas was granted immunity in return for his testimony at the court-martial of his subordinate Lieutenant Colonel Steven L.