Human remains have been found in the search zone where an Australian Army helicopter crashed into the sea in Queensland's Whitsundays last week.

The MRH90 Taipan ditched into the ocean south of Hamilton Island on Friday night during a training exercise.

Four crew - Captain Danniel Lyon, Lieutenant Maxwell Nugent, Warrant Officer Class Two Joseph Laycock and Corporal Alexander Naggs - were onboard.

On Thursday, Australian Defence Force Chief of Joint Operations Lieutenant General Greg Bilton said unidentified human remains had been found, but positive identification was unlikely to happen until more of the wreckage was located.

He said a remotely operated underwater vehicle had located a debris field that included parts of the cockpit about 40 metres below the surface.

"The debris field is consistent with a catastrophic, high impact [crash]. Sadly I can confirm unidentified human remains have also been observed in this location by the remote operated underwater vehicle.

"Due to the nature of the debris field, positive identification of the remains is unlikely to occur until we recover more of the wreckage."

Lieutenant General Bilton said all communications were "normal" before the aircraft hit the water.

He said the helicopter's black box had not yet been found.

"It's a difficult task but we will do our absolute best to find it - the black box is critical to helping us to understand what's actually taken place."

He said the army had spoken with the men's families and was providing them with support.

Lieutenant General Bilton said there had been difficult weather conditions in the search zone and these were expected to continue into the middle of next week.

"Both underwater and above the surface. The Whitsundays is renowned for its significant currents so the team are working through those and as you can see we are making progress, but it is methodical."

He said the loss of the four crewman was having a "significant impact" on the units.

"We're just making sure that we provide the sort of psychological support and the support for their well-being that's necessary," Lieutenant General Bilton said.

"Six aviation regiments have come together. I'm confident their commanders are working hard to work through the challenges that they confront in losing their mates."

On Monday, Deputy Prime Minister Richard Marles said there was no longer hope the men had survived, and the search and rescue had become a recovery mission.

The Taipan fleet has now been grounded, and will not fly again until it is understood what happened, he said.

Marles said the transition to Blackhawks had begun.

Asked how many Blackhawks were currently in Australia and how many pilots were certified to fly them, Lieutenant General Bilton said he was unable to give a "specific answer yet".

"We're still working through the plan on how we'll work that capability," he said.

He said a decision on the future of the MRH90s could not be made before there was an outcome to the crash investigation.

The MRH90s - which have had a troubled history - were due to come out of service at the end of this year.

- This story was first published by the ABC

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