Ambulances are being diverted from Perth's new Fiona Stanley Hospital and operating theatres have been closed because of flooding.

Flooding at Perth's new Fiona Stanley Hospital for the second time in less than three months has prompted ambulances to be diverted and operating theatres to be closed.

A main pipe that supplies ward towers burst in April, affecting access to hot water and the air conditioning system.

It is believed the flooding on Thursday has been caused by a similar problem.

A spokeswoman for the hospital described the mishap as a "large water leak", and said ambulances were being diverted and operating theatres closed as a temporary precaution.

She said repairs were underway and the hospital should return to the majority of its normal operations later on Thursday afternoon.

Health Minister Kim Hames said the latest flooding incident was very concerning.

"You'd have to ask now why we've had two sections of pipe burst, areas that are not of any particular note," Dr Hames said.

"The first one was a joiner - a part that's supposed to last for 100 years."

Opposition health spokesman Roger Cook said the public had a right to know what was going wrong at the hospital.

The flooding is the latest in a string of problems dogging the $2 billion hospital, including a surgical equipment contamination scare that resulted in Serco losing that part of its lucrative services contract.

Patient Jared Olsen, 41, died early this year after he was given the wrong drug.

A parliamentary inquiry into the hospital's services is currently being carried out.