The two servicemen -- a private and a corporal -- were hospitalised after escaping from the jaws of the reptile, which attacked in August 2021 when they went for a swim in Cape York Peninsula in northeastern Australia.
The pair had been given permission to go fishing in an inflatable Zodiac boat in the remote region, about 750km (450 miles) north of the Queensland city of Cairns.
After anchoring the boat, they jumped into the water and were "almost immediately" attacked by the crocodile, said Australia's work health and safety watchdog Comcare on Friday.
"The crocodile dragged one of the soldiers underwater and mauled him while his colleague fought off the animal, allowing the men to escape to the Zodiac," the government body said.
Both soldiers were badly injured, suffering bite and claw wounds, and they were treated at Cairns Hospital.
Prosecutors laid a single charge against the Department of Defence alleging it had breached federal work health and safety laws, Comcare said.
The department is accused of failing to implement a number of policies: prohibiting workers from entering crocodile-inhabited water without an operational or safety reason; doing risk assessments; and providing a detailed safety briefing about the risk of crocodile attacks.
The soldiers had been taking a landing craft from their base in Darwin to Townsville for maintenance when they decided to go for the ill-fated swim.
If found guilty, the maximum penalty is Aus$1.5 million (US$980,000).
The defence department thanked members of the community and emergency workers who helped the two men after the attack.
"The safety of our people is paramount in all activities and critical to our mission of defending Australia and its national interests," it said in a statement provided to AFP.
The defence department confirmed a single charge had been laid against it but declined further comment, citing the ongoing legal proceedings.
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