Gary Dickson said every year about half a dozen public-sector employees contact his office to report possible breaches.
Dickson said in his annual report Tuesday that in some cases, it is covering up a loss of personal information of clients or patients. In others it may be destruction of records to frustrate a possible access to information request, he said.
But those workers aren't protected and Dickson said his office has to tell them to proceed at their own risk.
"Usually they're quite anxious because there's huge consequences if their employer finds out that they're raising these things with an independent officer (of the legislature)," said Dickson.
"And we've had to say 'You need to know, we can do everything we can to protect your identity, but at some point, sometimes in an investigation, we need to reveal identity to be able to get to the bottom of it and you're not protected under the labour relations legislation.'"
The commissioner said Saskatchewan needs to protect whistleblowers from being fired or demoted if they act in good faith.
He recommended a whistleblower provision be included in privacy legislation similar to provisions in British Columbia, Alberta and Prince Edward Island.
Dickson said the purpose of whistleblowing is identify wrongdoing and that may not happen without protection.
"I don't for a moment mean to suggest it's common. I don't think it is," he said.
"The people we deal with take their jobs seriously and privacy and access rights seriously. But I think what happens is, if they're not able to do that in a safe fashion, they're not going to raise it and that may mean that there are breaches of Saskatchewan law that go unaddressed.
"And there may be no consequences when there well should be some consequences for wrongdoers."
Dickson also said it's time for the province to develop a new private sector privacy law. He noted that grocery store, car dealership, dry cleaner or other private business workers don't have the same kind of privacy protection as workers in the public sector.
The commissioner said it's time for Saskatchewan to follow the lead of Alberta and British Columbia and protect employees in the private sector.
"It would be actually a very simple matter to actually take that, Saskatchewanize it with some tweaks and it's a model set to go," he said.
Finally, Dickson said the 2011-2012 year has been a particularly challenging one for the health information file.
In March 2011, Dickson and two assistants had to wade through a massive recycling garbage bin behind a Regina mall to recover medical files. They found 180,169 pieces of personal health information, including approximately 2,682 patient files, in the recycling bin.
Dickson said the doctor involved lost track of the records before they were thrown into the recycling bin by two employees of a contracted maintenance company for the shopping centre.
The commissioner recommended nearly a year ago that justice officials prosecute Dr. Teik Im Ooi under the Health Information Protection Act.
The Saskatchewan government said Tuesday that the case is still with prosecutions branch and no decision has been made.