Speaking to the ABC's Stateline NSW programme on Friday, directors, clinicians and other heads from the service said they had "reservations about the quality of data" in their systems.
This made it difficult to make cost comparisons between them and other area health services nationally and to measure hospitals' performances.
"One of the problems with which we are faced is that because we've had to spend the money on pills, potions and blankets, we haven't been able to spend the money on getting good information services," said Dr Malcolm Fisher, a senior staff specialist in intensive care at Royal North Shore (RNS) hospital.
Dr John Vandervord, clinical director of surgery at RNS, described an instance where bad data impacted the hospital's reported theatre utilisation rates.
"We were always regarded as having very poor theatre utilisation; that is, we had theatres sitting empty because we didn't seem to have enough cases going through," Vandervord said.
"In fact, we were only recording the elective cases. We were not recording in that data our emergency cases, [which] are over 50 percent of what we do [in theatres]."
Dr Tony Joseph, chair of the medical staff council at RNS, conceded that while the average length of stay at the hospital "is perhaps equal or maybe one day longer than peer hospitals", he believed re-admission rates were also lower as a result.
"[But] we don't really know 'cause the data's not good enough to tell us if that's the case," Joseph said.
Dr Danny Stiel, gastroenterologist and clinical director division of medicine and aged care RNS, called for a review of data that measure hospital performance.
"Benchmarking or key performance indicators need to be more clinical than they are," Stiel said.
"Currently, our performance is rated upon things such as length of stay in the emergency department, [and the] time it takes to see a patient. They may be important issues and many of them are, but basic health outcomes like readmission rates aren't regarded as terribly important in the current benchmarking process.
"We need to redefine what we mean by a hospital performance as a clinical performance, not just a financial or a time one."