The auditor general's office is expressing frustration about the way Citizenship and Immigration Canada continues to hand out visas, and is concerned about delays on drug safety at Health Canada and planned spending by National Defence.

Overall, the report released Tuesday gives a passing grade to the Conservative government on how it tracked spending for three of the programs under its $47-billion Economic Action Plan introduced in 2009, but said it's not clear how the government is going to determine the effectiveness of one of them.

The report examined the $4-billion Infrastructure Stimulus Fund, the $2-billion Knowledge Infrastructure Program and the $1-billion Community Adjustment Fund.

Interim Auditor General John Wiersema is critical about the Department of National Defence and Citizenship and Immigration Canada in his report released Tuesday. (Adrian Wyld/Canadian Press)

"For the three specific programs we audited, the government was diligent in monitoring the progress of projects and their spending," Wiersema said at a news conference in Ottawa. "It also took corrective action as required to ensure that projects were completed as intended." His audit did not include an analysis of whether the projects funded were worthy of the cash, only if the money was properly tracked by the departments spending it.

The Conservatives have touted the EAP as a successful program that created jobs, but Wiersema's report says data was collected in a number of ways by various departments, making it difficult for the government to assess how well its goals were achieved.

The government is supposed to table a report in early 2012 to summarize the overall performance of the Economic Action Plan and Wiersema said at a news conference that his understanding is that the Conservatives are going to use economic modeling to come up with figures on how many jobs were created.

He acknowledged it is a difficult task to quantify how many jobs can specifically be tied to the EAP programs and said it's too early to tell if the government's final tally will be reliable. Accuracy will depend on how the government will estimate the job creation numbers and Wiersema said his office will take a close look at that report once it is submitted but he did not commit to doing any further audits of the EAP.

"The Economic Action Plan involved $47 billion of stimulus to the economy, I think it's really important that the government follow through on its commitment to report to Parliament on the overall success of the Economic Action Plan," he said.

Finance Minister Jim Flaherty said in question period that the government will table a final report and he defended his government's job-creation efforts saying 600,000 net new jobs have been created since the recession hit.

Opposition parties slammed the government throughout the day on the report's findings but ministers responsible for the various departments that were the subject of audits fended off the attacks.

Citizenship and Immigration Minister Jason Kenney said he shares some of the concerns identified in the report and that his department is already implementing its recommendations.

The fall report identified a number of problems when it came to Kenney's department and the Canada Border Services Agency (CBSA). Wiersema said they "need to do a much better job of managing the health, safety and security risks associated with issuing a visa."

Highlights of the AG's 2011 fall report The federal government did a 'good job' of monitoring billions spent under its Economic Action Plan, but must meet its pledge to report on the impact on job creation.

Citizenship and Immigration Canada and the Canada Border Services Agency must do a better job of managing health and safety risks when granting visas.

DND likely hasn’t set aside enough money to maintain and repair all the equipment it plans to buy over the next 20 years.

Health Canada is still not being timely or transparent enough when it comes to information about drug safety and clinical trials.

Wiersema said that the system lacks even the "basic elements" for visa officers to ensure that they get the right information to make the decision on whether to let someone into the country or not.

Flaws in visa-granting system

The audit identified a number of problems: it found that many of the criteria used by visa officers to identify high-risk applicants are outdated; CBSA analysts who provide security advice to visa officers have not received the necessary training; their work is rarely reviewed; and there was no evidence that mandatory checks were completed.

"We've been reporting on some of these problems with visas for 20 years and I find it disturbing that fundamental weaknesses still exist," he said."It's time that CIC and CBSA work together to resolve them."

Wiersema said the security manuals used by visa officers when making their decisions haven't been updated since 1999. The audit also pointed out that medical screening for danger to the public has focused on syphilis and tuberculosis for the past 50 years, even though health professionals are required to monitor and report on 56 diseases.

Citizenship and Immigration has not reviewed whether visa applicants should undergo mandatory testing for some of those diseases and it also doesn't review its decisions to grant visas later to ensure the right decisions were made.

"This means that CIC and CBSA don't know if a visa was issued to someone who was in fact inadmissible," Wiersema said.

The interim auditor general was asked at his news conference whether the flaws in the system means there are people who were granted entry to Canada who should have been kept out.

"The department is not able to provide us with assurance that that's not happening," he responded.

Defence maintenance plans scrutinized

The fall report also included an audit of how National Defence allocates money for the maintenance and repair of its equipment, and it found a number of deficiencies. The government plans to spend $60 billion on new equipment over the next 20 years and $140 billion on parts, maintenance and training, but the audit concludes National Defence lacks "complete, reliable and integrated information" on the total actual costs of maintenance and repair.

"The absence of this information impedes its ability to make informed decisions about the life-cycle management of its fleets or to determine whether it is putting enough funds each year into maintenance and repair," the audit says.

"There is a significant gap between the demand for maintenance and repair services and the funds made available," the report says. The audit says National Defence has indicated it is likely its plan for new equipment hasn't set aside enough money to maintain it.

Military procurement is a controversial topic on Parliament Hill because of the government's plan to buy 65 new F-35 fighter jets. Despite criticism from the opposition parties, the Conservatives have remained firm on their commitment to buy the planes.

The latest figures in the audit show that National Defence spends more than $2 billion per year to maintain its submarines, ships, aircraft and land vehicles, and the older the equipment becomes, the more expensive it is to fix it.

The audit says National Defence's ability to meet training and operational requirements over the long term is "at risk" because of weaknesses in how it is contracting maintenance and repair and poor management information systems.

The interim auditor general's fall report also examined Health Canada and how it regulates pharmaceutical drugs. It found the department is "struggling with the timeliness and the transparency" of some of its activities.

Health Canada slow to review potential safety risks

Health Canada has increased the amount of information it gives to the public on the drugs it approves, but the audit found it does not provide enough information on rejected submissions or on applications withdrawn by the manufacturer. It is also failing to live up to a longstanding commitment to be more transparent about the information related to clinical trials.

Wiersema's office also said Health Canada is slow to assess potential safety issues it identifies with drugs on the market and it can sometimes take up to two years to complete a review.

"We think it's a serious issue ... I think two years is too long," he said.

Opposition MPs accused the government of putting safety at risk but Health Minister Leona Aglukkaq told the House of Commons that she agrees with the audit's findings and that work has been underway for some time to ensure the products on drug store shelves are safe.

Another program reviewed by the auditor general was the Tobacco Transition Program at Agriculture and Agri-Food Canada that was announced in 2008.

By May 2009 $284 million had been paid to farmers to help them get out of the industry and the audit has found that setting up the program was a rushed job and not enough safeguards were put in place to ensure the program wasn't misused.

As a result, there were no controls to ensure that farmers in the program couldn't make business arrangements that would undermine the program, such as renting out their land to family members. The department didn't properly prepare for risks associated with the program and producers didn't clearly understand how it was supposed to work.

The audit also examined other programs at the department that help protect farmers against big drops in income and found ongoing problems. Farmers can wait up to two years for a payment they are owed and the amount of the payments is hard to predict, the review concluded.