The builder of the delayed Perth Children's Hospital claims construction is finished but Health Minister Roger Cook says patients won't move in until the drinking water is deemed safe.

The $1.2 billion building is more than a year overdue, with lead in the drinking water, asbestos in roof panels and non-compliant fire doors all contributing to the hold-up.

Mr Cook said head contractor John Holland may have reached a contractual milestone but the state government would need to deem the water supply lead-free before transferring patients from Princess Margaret Hospital.

“They (John Holland) might have satisfied themselves that they’ve resolved the lead-related issues but the one person that needs to be convinced of these things is the water regulator, the chief health officer,” Mr Cook told 6PR on Tuesday.

Australian Medical Association WA president Andrew Miller said the state government was right to take a cautious approach.

“If they get in there and find that they still have problems down the track and they have ward closures and there’s building works going on, that’s going to be a disaster,” he told the broadcaster.

Reports of the lead contamination emerged in September.