A new problem has struck the trouble-plagued Perth Children's Hospital with the potentially deadly legionella bacteria detected during routine water testing, as the Health Department grapples with an ongoing lead contamination issue.

Child and Adolescent Health Service chief executive Robyn Lawrence confirmed to the ABC that 14 instances of legionella had been found.

The bacteria was discovered in warm water outlets, a shower head and a drinking water fountain.

Legionella is found naturally in lakes and streams but can become a health concern when it grows and spreads in human-made water systems, including large plumbing systems.

People can contract Legionnaires' disease — a severe, occasionally lethal form of pneumonia — when they breathe in small droplets of water that contain the bacteria.

Last year, one man died and 15 people contracted Legionnaires' disease when the bacteria was discovered in two water cooler towers in the Sydney CBD.

The WA Australian Medical Association President Omar Khorshid said a Legionnaires' disease outbreak could be serious.

"There have been deaths in Australia," Dr Khorshid said.

"Generally in people who are susceptible to respiratory diseases like the elderly or people with lung disease.

"Unfortunately though legionnaires can affect the young and it can affect the healthy, so it's very important to have it eradicated from the water systems."

In a statement Dr Lawrence the "results detected were at the low end of the accepted scale" and the relevant authority would implement remediation strategies, but she did not detail what that would involve.

"The finding of Legionella in a water system is an identification of possible risk, not direct or immediate consequence to patients or other users of the water supply," she said.

The positive samples were collected on October 19 and 20.

"The likely reason is a combination of low hot water temperatures and restricted flow due blocked aerators/inline strainers and/or a lack of flushing resulting in a biofilm build-up at the outlet that harbours and supports the colonisation of legionella," she said.

A litany of problems

It is the latest in a string of issues for the hospital, ranging from asbestos in the roof panels to contractor disputes and faulty water piping.

The main issue that has prevented the hospital opening is lead contamination in the drinking water, which remains unresolved.

A brass fitting taken from the new Perth Children's Hospital during an investigation into the cause of lead contamination in the water at the facility. The picture was released in a report by the Chief Health Officer into the contamination problem, along with the following caption: "An example of visible corrosion product on the internal surface of a Cold TMV Inlet Elbow Connector". ( Supplied: Chief Health Officer )

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 is currently costing taxpayers $6 million a month as it sits idle with no patients — that includes about $6000 a day in power bills and $700,000 a month to contractor Capella Parking for car bays that are sitting idle.

On top of these issues, WA health officials recently admitted a raft of other construction issues at the hospital during a budget estimates committee hearing.

These included problems at the on-site childcare facility, mental health unit, isolation rooms and anaesthetic gas delivery.

The WA Government is bracing itself for a lengthy legal battle in its bid to recoup millions of dollars from the head contractor of the hospital, John Holland, over long delays to the project.

John Holland in return is seeking $300 million in compensation from the Government for changes to the project.

The $1.2 billion project is now running more than two years behind schedule, and is not expected to open until the first half of 2018.