A costly wastewater recycling plant installed at the trouble-plagued Perth Children's Hospital is likely to stay switched off due to Heath Department fears of cross-contamination.

The $230,000 wastewater treatment facility is designed to treat used shower-water with ultraviolet light and chlorine to use it for flushing hospital toilets.

However, the Department of Health has questioned the use of recycled water due to the increased risk of exposure to dangerous pathogens present in a hospital setting.

And it claims builder John Holland installed the system without approval which put it in breach of department guidelines.

The problem-prone $1.2 billion hospital was originally due to be completed in 2015 but has suffered from issues including water contaminated with lead and potentially deadly legionella bacteria, asbestos in roof panels and non-compliant fire doors.

Health Minister Roger Cook says the latest kerfuffle is proof of “the level of project mismanagement” by the previous Barnett Liberal government.

A health department spokeswoman says it considered a draft proposal for the system and found it presented, “a high-exposure risk level” based on guidelines for recycled Water in WA in 2011.

The department advised that given the low volumes of recycled water to be treated and the increased pathogen risk that the “proposal should be re-considered,” she said.

She added the cost of running and maintaining the system also outweighed any potential savings.

The spokeswoman said main contractor John Holland had asserted it thought approval from the department was only required prior to turning the system on, not before it was installed.

The system is currently bypassing recycled water outside the system to the sewer drainage network.

The Health Minister says he is aware the greywater system is in place but said it would not be commissioned until further reviews by his department.

But Opposition Health spokesman Sean L’Estrange accused Mr Cook of unnecessarily increasing public concern the hospital’s opening would suffer further delays.

“Why is the Labor government, and Minister Cook, out there playing the blame game…when it’s not even being used?”

He also questioned the department’s claim it was unaware the recycling system was being installed.

“The department of health were intimately involved in the designing of this particular hospital,” he said.

Mr Cook says he would wait for the department’s final recommendation once they go through the correct channels.

The final draft of the proposal is being reviewed and will be submitted shortly to the department for approval.

By Sophie Moore