Police have referred allegations against an ABC journalist relating to the Afghan Files to prosecutors, the public broadcaster says.
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ABC managing director David Anderson said it was a "disappointing and disturbing development" and the broadcaster was fully backing its reporter, Dan Oakes.
"The allegations concern Dan's reporting on the series of stories published by the ABC in 2017 known as the Afghan Files. They were also what prompted the AFP's extraordinary raid on the ABC's Ultimo headquarters last year," he said in a statement.
"This is a disappointing and disturbing development. The Afghan Files is factual and important reporting which exposed allegations about Australian soldiers committing war crimes in Afghanistan. Its accuracy has never been challenged."
He said the ABC had been advised the AFP was referring allegations Oakes to the Commonwealth Director of Public Prosecutions. However, it would not be taking any further action against ABC journalist Sam Clark, who also worked on the Afghan Files.
"The ABC fully backs Dan and we will continue to support him however we can. Doing accurate journalism that is clearly in the public interest should not be an offence," Mr Anderson said.
Oakes tweeted that whether or not he was eventually charged, "the most important thing is that those who broke our laws and the laws of armed conflict are held to account. Our nation should be better."
The journalists' union, the Media Entertainment and Arts Alliance, called on Attorney-General Christian Porter to "demonstrate the government is committed to press freedom by calling an end to the investigation and possible prosecution of a journalist for reporting the truth".
MEAA Media federal president Marcus Strom said it was particularly cruel that Oakes and Clark had had to wait so long to learn what would happen to them.
"It's three years since the Afghan Files story broke and a year since the AFP raid. And yet, government agencies have moved with greater speed against a whistleblower and a journalist than they have in their investigation into the alleged war crimes," he said.
"The ABC's journalism clearly embarrassed the government and the Department of Defence because they had classified the war crimes allegations as 'secret' so it could be hidden from the public. In fact, the story needed to be told because it was clearly in the public interest.
"We now know, from subsequent news stories, that there are multiple allegations of war crimes under investigation. And yet it is the truth tellers who face jail time."
The ABC was raided in July last year over stories published in 2017 that suggested Australian troops may have committed war crimes. They were based on leaked Defence Department papers.
At the time of the raid, ABC editorial director Craig McMurtrie said officers were relying on a section of the Crimes Act that did not include a public interest defence when the stories were published.
The raid came a day after the AFP searched the home, computer and mobile phone of News Corp journalist Annika Smethurst over a story she wrote last year detailing an alleged government proposal to spy on Australians.
The ABC challenged the warrants in the courts, arguing it had been "legally unreasonable" for federal police to seek a warrant to search its head office and for a registrar to grant it.
It argued the conditions of the warrant were too broad and "materially misstate the terms of the suspected offences". The ABC also contended that journalistic privilege and the right to protect sources should endure despite whistleblower David McBride admitting publicly that he leaked the Afghan files.
However, it lost the federal court case. It initially considered appealing the decision, saying it gave police the right to "enter a newsroom and fossick around for confidential files".
Several journalists expressed their shock and frustration at Thursday's decision.