The builder of the troubled Perth Children's Hospital (PCH) project will be forced to pay tens of millions of dollars to the WA Government as a result of delays to the project, according to the state's top legal adviser.

Acting state solicitor Nicholas Egan told a parliamentary inquiry into problems with the PCH project that clauses within the construction contract dictated head contractor John Holland would be liable to pay the state at least $42.5 million.

But the state is hoping to eventually recover much more than that from John Holland, to cover the costs of work to remedy lead contamination in water and other construction problems.

The hospital is now almost two years behind schedule and the Government estimates every month the facility sits vacant costs it an extra $6 million.

Mr Egan told the hearing clauses in the contract dictated John Holland would be liable to pay $180,000 for each day the hospital was delayed, capped at $42.5 million.

That $180,000 per day figure started from August 31, 2015 meaning the $42.5 million cap was reached more than a year ago.

The Government is now bracing for a lengthy legal battle to recover additional costs, with John Holland previously insisting the source of lead contamination was outside the hospital and therefore the problem was not its fault.

John Holland has declined to comment.

John Holland's delivery record 'woeful'

Earlier, WA's top health bureaucrat took a significant swipe at John Holland over mounting delays to the project.

In his evidence to the inquiry, WA Health director-general David Russell-Weisz said John Holland had a "woeful" record in terms of delivering projects on time and was an "unreliable builder".

"We have been consistently frustrated by the construction element of this program," he said after the hearing.

"It [John Holland's performance] is clearly not up to scratch, we want to be open and we are not open."

It also emerged during the hearing that the top bureaucrats overseeing the $1.2 billion project were not told about the lead problem until three months after it first emerged.

Mr Egan was critical of the delay in the taskforce overseeing the project, which included Dr Russell-Weisz and other top bureaucrats, being told about the problem.

"It should have been elevated to taskforce much sooner than it was," he said.

Health Minister Roger Cook has previously said a timeline would be set for the hospital's opening in November, but it certainly would not be taking patients this year.

Work to replace plumbing parts identified by the Government as the source of lead is yet to commence.