Operating theatres at Perth's new Fiona Stanley are sometimes left uncleaned, a parliamentary inquiry has been told.

A parliamentary inquiry has heard of ongoing woes at Perth's new Fiona Stanley Hospital including unsanitary operating theatres and staff "drowning in paperwork".

Melissa Wagner, the Health Services Union's senior organiser for the public sector, told the inquiry on Wednesday that theatres were sometimes found not cleaned, particularly on Monday mornings and evenings.

Ms Wagner said the service was outsourced to Serco and there was a lack of transparency about the company's standards.

Serco was stripped of its equipment sterilisation contract at the hospital in April, but still has about 20 contracts for other work.

The union's lead organiser for the public sector, Richard Barlow, put that down to the team's inexperience.

"They really didn't know what they were doing," Mr Barlow said.

The inquiry was also told of major problems with the IT system at the hospital, which was originally intended to be a "paperless" facility.

Various systems were incompatible, which meant, for instance, that a patient's fluid balancing records had to be manually transferred when they moved from the intensive care unit into the general wards.

One worker had complained he was "drowning in paper".

Secretary Dan Hill said the state government needed to dedicate whatever resources were needed to fix the IT system.

The inquiry was also told that patients at the amputee and limb centre were restricted to five physiotherapy sessions whether they needed more or not, then referred elsewhere.

The parliamentary committee also heard that the wait time for outpatient pharmaceutical dispensing at Fiona Stanley Hospital was double that of other Perth hospitals at more than two hours.