Acting auditor Judy Ferguson says the government started the system in 1997 and it doesn't know when it will be done or how much it will cost.
The provincial government has so far spent $502 million on the system.
Ferguson says different health regions are at different stages of implementation, which is causing lots of problems.
The report says some patients carry their own records between hospitals and clinics because a comprehensive record of their health information is not accessible between different health regions and organizations.
Ferguson calls gaps in the system “troubling,” adding that they create delays in patient care and can lead to duplicate and unnecessary medical tests.
“In order to realize those benefits, you have to get it substantively done,” said Ferguson.
She wants to see the province standardize the data that goes into the electronic record. Ferguson also says more money needs to be pumped into the technology that is needed for the system to flourish.
Ferguson also wants the government to implement a multi-year operational plan.
The auditor's report also touched on wastewater system regulation. It outlined ways the Water Security Agency can better regulate public wastewater systems so that risks to the environment and the public from improperly treated wastewater are reduced.