Ambulances have been diverted from Peel Health Campus and a number of patients relocated after black mould was detected at the Mandurah hospital.
The mould was found in the air-conditioning system on Thursday prompting the hospital to transfer 32 patients to Rockingham and Fiona Stanley Hospitals.
Ambulances to the emergency department were also diverted while three operating theatres had to be shut down.
The emergency department remained open for walk-ins.
The maternity and paediatric units, some wards, consulting rooms and the kitchen were not affected.
A Peel Health Campus spokesperson said a thorough cleaning process is underway.
"We have undertaken an initial disinfection of the air conditioning system including the air handling units and are awaiting feedback from the Environmental Health Unit about any further steps we need to take," the spokesperson said.
"Once we have approval, we will then implement a broader, comprehensive cleaning regime which includes disinfecting the rest of the impacted areas of the hospital.
"We have a maintenance and cleaning program of the air conditioning filters in place which we are compliant with. Moulds are commonly found in the community and are regularly identified in air conditioning units."
As a precaution, staff and patients are also required to wear PPE and visitors are being temporarily restricted.
"The community can be reassured that moulds are commonly found in the general environment and in most cases with a healthy person, their immune system can protect them from infection," a Peel Health Campus spokesperson said.
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