A $1-million CT simulator was soaked, and is currently in pieces, after a heating pipe burst in the Dickson building at the Victoria General site.
The machine was soaked and the manufacturer has been brought in to help with the assessment of the expensive piece of equipment, which was bought new in 2008.
The flood has also forced many medical appointments to be postponed.
Capital District Health Authority spokesman John Gillis said a heating pipe on the fourth floor burst on Saturday, sending water through two floors below. The Dickson building is on the Victoria General Hospital site.
In a statement Gillis said a CT simulator used to plan radiation treatments is out of service until it can be tested for damage. The health authority also said some staff had to be moved to temporary offices because of the damage.
Capital Health says everyone with an appointment that's changed has been notified. Cleaning crews began mopping up on Saturday night.
The Dickson building houses the Nova Scotia Cancer Centre.