The acting prime minister said it was important to allow federal police to follow through on the evidence unearthed by former NSW judge Paul Brereton.
"It is dealing with a shameful episode in Australia's military history," Mr Marles told Sky News on Sunday.
"It matters in terms of who we are as a nation, who we are as a people, that our country deals with this itself."
Asked when Australians can expect charges laid as a result of the inquiry, Mr Marles said he would commit to following through with the inquiry to its completion.
"There is going to be no stepping back in relation to this because it is fundamentally important process for how we are as a nation," he said.
Mr Marles has previously suggested he won't reverse former defence minister Peter Dutton's decision not to strip defence personnel of meritorious unit citation, despite the original recommendation from defence leadership.
An Office of the Special Investigator is working with the Australian Federal Police to investigate allegations of criminal offences by ADF members in Afghanistan from 2005 to 2016.
Last year's scathing Brereton inquiry unearthed credible evidence of war crimes by Australian special forces while serving in Afghanistan, including 39 murders.
This includes allegations soldiers tortured two prisoners with junior patrol members ordered to carry out executions.
In one of the most gruesome allegations, Australian soldiers cut the throats of two 14-year-old boys and dumped their bodies in a river because they believed they were Taliban sympathisers.
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