Health authorities have moved to reassure the public the Perth Children's Hospital's planned opening remains on track, despite potentially deadly legionella bacteria being discovered in the $1.2 billion facility for the second time.

However, Child and Adolescent Health Service chief executive Robyn Lawrence said she could not give a guarantee that it would not face further delays, with authorities reviewing the situation on a daily basis.

"At this stage we remain on track, we will continue every single day right up to the final patient move day to consider the risks of remaining in our current hospital versus what's happening at our new hospital so that any move occurs only if it's safe to do so," Dr Lawrence said.

"In any move there's a risk that we might have to change it, there could be a substantial event out in the community which could cause us to change our plans.

"At this stage I reinforce we remain on schedule."

In an email to senior staff sent on Friday, Dr Lawrence said legionella had been detected in 45 of 100 sampled locations and steps to rectify the problem were "immediately" taken, including turning off the water supply and raising the temperature of the hot water system.

Another type of bacteria, Pseudomonas aeruginosa — which can cause serious infections in people with weak immune systems — was detected at 11 locations.

The samples were collected on April 16, just eight days after Premier Mark McGowan and Health Minister Roger Cook toured the facility and made a point of being seen drinking from fountains.

"We have decided to temporarily stop using the water supply at PCH today, which will allow us to intensively treat the water," Dr Lawrence wrote.

"Staff will be supplied with bottled water to enable this to occur and until we can confirm that the water is safe.

"Please be assured the safety of our staff and future patients remains our priority."

Staff changerooms were also closed and all shower heads were cleaned as a precaution.

Legionella bacteria was first discovered in October last year at multiple sites throughout the hospital, including a shower head, warm water outlets and a drinking fountain.

Last month Premier Mark McGowan and Health Minister Roger Cook drank water at the hospital. ( ABC News: David Weber )

The detected levels of the Legionella bacteria are similar to those found last year.

Opening date remains 'for now'

The $1.2 billion hospital is due to begin a staged intake of patients in nine days, beginning with outpatient clinics.

Legionella bacteria live in lakes and streams, but can also grow in pipes and other water infrastructure.

If water containing the bacteria is inhaled, it can cause Legionnaires' disease — a severe form of pneumonia.

Dr Lawrence said the opening schedule for the hospital would remain in place for now, with authorities to reassess the situation early next week.

Australian Medical Association WA president Omar Khorshid said he was disappointed to hear of the latest discovery of legionella bacteria, but believed it would not delay the hospital's opening.

"We remain confident that following remedial action being taken by the Health Department, the planned dates for the treating of outpatients and the formal opening of the new hospital will still be met," Dr Khorshid said.

"We have also been reassured by the CEO of the PCH that this is not an unusual situation in new buildings when water is sometimes stagnant for long periods."

Opposition health spokesman Sean L'Estrange said the Government needed to be more transparent about problems at the hospital.

"They set their standard of disclosure to be gold standard, that was Premier McGowan's commitment to the people of Western Australia when he took office," Mr L'Estrange said.

"[Yet] here we are finding out 45 out of 100 samples have legionella bacteria and we're finding out about this through a leaked email, we're not finding out about this with open and transparent commentary from the Minister or the Premier."

Litany of problems

The discovery of the two bacteria — both of which can cause serious illness in immunocompromised people — is a major blow for the hospital, given the proximity to its opening and the litany of past problems that have delayed the project by almost three years.

These include the discovery of asbestos in the roof panels, contractor disputes and faulty water piping.

The hospital's lead contamination issue was resolved in March. ( ABC News: David Weber )

The main issue that prevented the hospital opening was lead contamination in the drinking water, which was finally resolved in March.

The basement of the hospital has been flooded by a burst pipe, 900 fire doors have had to be ripped out and replaced, and key members of the hospital's leadership team have resigned.

It has cost taxpayers $6 million a month to sit idle with no patients — that includes about $6,000 a day in power bills and $700,000 a month to contractor Capella Parking for car bays that are sitting idle.

There have also been a raft of other construction issues at the hospital, including problems at the on-site childcare facility, mental health unit, isolation rooms and with anaesthetic gas delivery.

Nearly three years of delays to the opening have cost the state more than $115 million.

That includes more than $20 million in compensation payments for the operators of the empty hospital car park.