The matter was briefly heard in Brisbane Magistrates Court on Friday and the department was due to enter a plea but instead applied for adjournment.

The department requested the court to rule on a strike-out application to challenge part of the set of facts that the prosecution would rely on during the case.

The exact facts that the department wanted to challenge were not disclosed in court.

Magistrate Joseph Pinder said it was a "fairly discrete issue" and he was not sure determining the outcome would require a hearing that lasted half a day, as was requested by both parties.

The Darwin-based army personnel were transporting a landing craft from Darwin to Townsville for maintenance in August 2021.

The soldiers, a private in his 20s and a corporal in his early 30s, were given permission to go fishing at the Cape York Peninsula community of Portland Road in a defence inflatable Zodiac, the federal workers' compensation and safety regulator Comcare said earlier.

"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," Comcare said.

The Department of Defence is charged under the Work Health and Safety Act for allegedly failing to provide a safe workplace or properly train its workers.

It is further alleged Defence failed to conduct a risk assessment or provide a detailed safety briefing about the risk of crocodile attack.

The charge carries a maximum penalty of $1.5 million.

A court hearing on March 25 will determine the strike out-application.