WA taxpayers have already forked out more than $15 million in penalties to the operators of a carpark at Perth Children's Hospital, which sat empty for nearly two years.

Now the cost to the State Government will continue to climb by hundreds of thousands of dollars over the next month, even though the hospital was officially opened last week.

New figures provided by the Government confirmed the cost of penalties under the contract with Capella Parking for the underground carpark at PCH now totalled $15.8 million — or more than $700,000 per month.

A Government spokesman also confirmed the official opening of the facility and the commencement of outpatient treatment was not enough to stop those penalties being charged.

Under the contract with Capella, the Government is liable to pay a penalty unless a certain number of hospital beds are functional on the site — a condition that will not be met until the facility's full opening in June.

The underground carpark at the centre of the contract is now open, having sat closed for nearly two years while Capella received those penalty payments.

The new Perth Children's Hospital will be fully opened by June 10. ( ABC News: Darren Dunstan )

Australian Medical Association WA president Omar Khorshid said it was crucial the mistakes of the carpark contract were not repeated.

"It is so disappointing that we are still forking out hundreds of thousands of dollars," Dr Khorshid said.

"It is not a great message for staff or the taxpayers of WA to know so much money has been wasted … in ways that seem at face value to be completely avoidable."

The carpark contract was struck by the former Barnett government and defended at the time as "a good deal".

But Opposition Leader and former treasurer Mike Nahan admitted it had turned out badly for taxpayers.

"Are (public-private partnerships) like that suitable? Yes. Was the risk assessment adequately done? Don't know. But did the risk come against us? Yes it did," he said.

Premier Mark McGowan said the contract was a bad deal that his Government was stuck with.

The staged opening of the hospital will continue over the coming weeks, with elective surgery commencing on May 28 and the emergency room following on June 10.