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Defence officials have been accused of mishandling soldier's bodies, losing remains of insurgents and illegally detaining children in Afghanistan.
Australian Defence Force (ADF) investigators allegedly wrongly placed three soldiers' bodies in the lids of caskets, according to an investigation by News Limited.
The allegations outlined by whistleblowers have sparked defence probes after reports of remains of suspected insurgents who died in custody being lost and deaths in custody not being investigated.
Other allegations include the illegal detention of a child, failure to investigate the shooting of a prisoner during interrogation and the 50-day detention of a critically wounded suspect.
Whistleblowers recount disrespectful handling of an Afghan corpse that was sent out of Tarin Kowt military base in a taxi with its legs hanging out the window, with the corpse never traced.
The incident was confirmed by Defence Chief General David Hurley, who blamed Dutch and Afghan authorities, but maintains a funeral service for the body had been held.
The soldiers involved in the casket lid controversy were Lieutenant Michael Fussell, Sergeant Brett Wood and Lance-Corporal Andrew Jones, the paper reports.
"The incorrect orientation of the caskets was probably due to a training deficiency that resulted in a lack of familiarity by some members with the unusual configuration of the caskets - that is that the lid is larger than the base," the ADF told the paper.
It added that it had developed more specific guidance on its responsibilities in the management of local human remains.