Australia's new army and navy helicopters have been proving difficult to start and stop in strong winds.

The Defence Department has acknowledged there were problems with the MRH90 Taipans — a multi-role helicopter — during recent flight trials.

"Some issues were encountered starting and stopping rotors under certain environmental conditions," the Department said in a statement emailed to the ABC.

The new helicopters have been involved in sea trials of the amphibious assault ship HMAS Canberra, which has six spots for medium-sized helicopters.

The Australian newspaper, citing unnamed sources, reported the design of amphibious assault ships served to accentuate wind conditions that affected helicopter rotors at slow speed.

HMAS Canberra is as big as a container ship, with a flight deck more than 200 metres long.

Dr Andrew Davies from the Australian Strategic Policy Institute (ASPI), who has been following the development of the nation's new helicopter fleet, was surprised there was an issue with ship-born operations.

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He noted helicopters similar to the ones assembled in Brisbane, by a unit of Europe's Airbus Group, operated on ships in Europe.

"In Europe there are helicopters flying off frigates. In fact, the naval version is the NATO frigate helicopter," he said.

According to Airbus Group's website, the 10-tonne MRH90, which can fly as fast as 300 kilometres an hour, can carry two pilots, two loadmasters and 18 combat troops.

The Royal Australian Navy has ordered six helicopters and the Australian Army has ordered 40.

Decision to acquire MRH90 'poor'

Last week, in a speech to an army conference, Dr Davies questioned the Federal Government's decision a decade ago to acquire the MRH90.

"I thought that this particular acquisition decision was an especially poor one and it wasn't the helicopter that the army wanted," he said.

The ASPI research director said the army wanted a helicopter from the Black Hawk family but a decision was made at cabinet level to pick the European helicopter.

Dr Davies suspected the lure of local jobs had swayed the decision.

The company has declined to comment on current issues such as stopping and starting the helicopters.

Australia Defence Association executive director Neil James was not prepared to write off the newly acquired choppers, which he noted were being used on a new ship.

"It's not clear yet whether it's a problem with the ship, a problem with the way the ship is used — which is probably the most likely — or a problem with helicopters themselves," he said.

Defence Department said in its statement the development of a suitable starting and stopping envelope for operations "remains a work in progress".