The Chief of the Defence Force has condemned News Limited papers for publishing stories about the alleged mishandling of Australian soldiers' remains.

The newspapers are reporting that the bodies of three soldiers killed in Afghanistan were mistakenly placed in upside down caskets for their return.

The reports claim there has been a "litany of errors" in the handling of Australia's war dead.

The claims drew an angry response from ADF Chief General David Hurley.

He told a Senate estimates committee on Monday that all bodies have been treated with the utmost dignity and respect, and the newspaper reports are "un-Australian".

"This is not an issue about the reputation of the ADF," he said.

"This is 32 families and extended families and the members of the ADF - soldiers and airmen - who accompanied those men on the way back and the enormous distress that this story could cause."

But he admitted that "on three occasions, once in 2008 and twice in 2011, caskets were used incorrectly during the initial part of the return journey from Afghanistan".

"In two instances, the orientation of the caskets was corrected when the remains were transferred to mortuary facilities ... and in the third case the error was corrected before departing the airbase in the [United Arab Emirates]," he said.

"Let me make it very clear that all inquiries to date have shown that the bodies were treated with the utmost respect and dignity.

"Importantly, the evidence to date indicates that the bodies were correctly oriented in the caskets at all times.

"Statements from the Australian Defence Force personnel who escorted and cared for these men on their return journey support this.

"Let me make it very clear again that at no time during these procedures has a misalignment of the bodies been identified and at no time since 2008 has Defence received any advice from Australian coronial authorities to indicate the bodies of ADF members were transported incorrectly."

General Hurley said the newspaper reports did not reflect the extreme steps Defence takes to recognise the dignity of its war dead.

"In speaking to the families concerned over the past few days, their reactions to the intention to publish this story have ranged from un-Australian to incredibly insensitive," he said.

"All three families have expressed their disgust that a newspaper would seek a to make a story of these issues.

"Publication today is particularly insensitive given two of the families are trying to deal with the first anniversary of their loved ones' death."

He said the "issue of the orientation of caskets was raised in mid-2011 and is the subject of an Inspector-General Australian Defence Force inquiry initiated in January 2012".

"The cause of the incorrect orientation of the caskets on these three occasions is subject to an inquiry by the Inspector General ADF," he said.

"As one family member put it, it was an honest mistake that was quickly corrected.

"Clear guidance on the correct use of caskets has been issued and I will keep you and the Government informed of this matter."