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Interim auditor general John Wiersema holds a news conference following the release of an audit report in Ottawa on Tuesday, November 22, 2011.Sean Kilpatrick

The public is waiting far too long to be warned about significant risks in the drugs they take, the federal Auditor-General said Tuesday.

It's only the latest example of risk caused by rampant information mismanagement that is undercutting work in many federal departments, said interim Auditor-General John Wiersema.

He called on the government to ensure things don't get worse as it goes about a major cost-cutting exercise over the coming years.

"We have found that poor information is a widespread, chronic problem in the federal government," Mr. Wiersema says in an overview of government operations.

"Managers are not systematically collecting and using the information they need to manage their programs, and they are not held accountable for this."

The audit of Health Canada found the department has an archaic system for monitoring that can take years to tell the public that some drugs already on the market come with significant risks.

In one case, a drug being prescribed for epilepsy, migraines, psychiatric conditions and weight loss was found to be linked to birth defects.

But it took six months for the brand-name drug to include a warning, and almost two years for generic producers to be told they had to change their labels and warnings.

In another case, the United States was already warning in 2006 that the long-term benefits of low-dose ASA could be eroded by taking ibuprofen at the same time.

But in Canada, a review took more than three years, and orders to change labelling for the public are still not fully in place for several hundred products that are affected.

"Health Canada is slow to act on potential safety issues related to drugs already on the market," Mr. Wiersema said in a release.

"It needs to get safety information out to Canadians more quickly, and address the potential for conflict of interest."

The Auditor-General also raised concerns about Health Canada failing to say why it rejected certain drugs, or required changes. Since doctors can prescribe drugs for conditions that have not been authorized, they need to have this information to keep their patients safe.

"It is important that they be informed when the department rejects a marketed drug for a new use, so they understand the department's concerns," says the audit, tabled in Parliament on Tuesday.

Health Canada says it has agreed to all the Auditor-General's recommendations and issued a statement saying Canada has "one of the safest and most rigorous drug safety systems in the world.

The fall report also highlighted problems in other departments:

— Canada's visa officers are failing to screen applicants for dozens of diseases, concentrating instead on just two diseases that were prevalent 50 years ago.

— The government has failed to properly monitor how effectively funds were spent under the recession-fighting Economic Action Plan, including information about just how many jobs were created.

— The military is doing a poor job of predicting its maintenance needs and costs over the long haul.

But the report on Health Canada raises the most disturbing issues. It found there is poor communication about clinical trials, pointing out that Health Canada was not disclosing information about authorized trials – depriving some Canadians with life-threatening diseases of a chance to participate in new treatment options.

The department is also not communicating with the public about unauthorized trials, making it impossible for participants to make informed decisions, the report said.

"This increases the risk that Canadians may be unaware of new treatment options or may unknowingly participate in an unauthorized trial."

In one case, a child was involved in an unauthorized experiment, but did not realize it until his parents contacted Health Canada with concerns about safety. Only then did Health Canada conduct an investigation.

"New procedures are being put to improve transparency," said Health Minister Leona Aglukkaq.

Opposition critics were quick to pounce, accusing the government of toying with patients' health and safety.

"It is taking the Harper government years to let health-care providers and the public know of safety risks involving prescription drugs," Liberal health critic Hedy Fry said in a release.

"Furthermore, the government has broken its promise to increase transparency in the drug-approval process. These shortcomings are placing the health and well being of Canadians in serious danger."

The audit shows a department overwhelmed with a mounting pile of information about thousands of drugs that are increasingly central in how Canadians manage their health care.

The department often receives crucial information about adverse reactions by fax or courier, and has to enter the information manually into a database. With the number of reports of adverse reactions skyrocketing in the last few years, the backlog is growing and Health Canada has not found a way to prioritize, the audit says.

The department is also falling behind on its inspections of clinical trial sites.

And its reviews of drugs for safety, efficiency and quality drag on, especially for generic drugs, over-the-counter medications and other drugs that are adjusted after they hit the market.

As for conflict of interest, the audit says Health Canada should beef up its requirements and actively make sure its employees are in compliance.

Health Canada says it has agreed to all of the Auditor-General's recommendations, and in some cases has already begun implementing them.

Indeed, Mr. Wiersema held out hope that new user fees charged to pharmaceutical companies for Health Canada's approvals will help resolve the government's lack of resources and huge workload.

The drug market in Canada is enormous, as Canadians have become more dependent on pharmaceuticals to treat their ailments. In 2008, there were 13,000 different kinds of prescription and non-prescription drugs sold in Canada for about $28-billion. Prescription drugs account for some 84 per cent of the total.

In 2010, doctors issued 505 million prescriptions.

Medication is becoming more complex and more diverse, posing a huge burden on regulators around the world, added Jeff Poston, executive director of the Canadian Pharmacists Association.