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Sheila Fraser's report on the federal government's national security efforts was delivered to Parliament Tuesday afternoon.
"These are not the kind of problems that can be fixed overnight," Fraser told reporters.
"What's the most disappointing is that these are systems and procedures that should be working well," Fraser later told CBC Newsworld.
Sheila Fraser in Ottawa
"We would have expected them to be given the priority they deserved."
The auditor general said, for example, border guards should know more about missing passports.
About 25,000 passports are lost or stolen each year, and front-line officers have no access to information about them, the report says.
The report said "watch lists" immigration officers use to screen applicants are inaccurate and poorly updated.
And federal agencies don't share information effectively which causes a number of concerns.
For one, Transport Canada can't fully access the RCMP's criminal intelligence when screening airport workers. Because of that, the auditor general found 4,500 people with access to restricted areas at five major airports have criminal associations worth investigating.
In the wake of the Sept. 11, 2001, attacks, Ottawa put together a plan to beef up security at a cost of $7.7 billion over five years.
The auditor general says some initiatives were poorly thought through. A digital system for gathering fingerprints, for instance, was hamstrung because no money was put into processing the information.
Fraser said her department looked at the security and anti-terrorism efforts of other countries, and found Canada was doing no worse than most, but she warned that was no reason for complacency.
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The Liberals say they've been working since Paul Martin became prime minister to improve the situation.
Martin consolidated several departments under the umbrella of a single minister, Public Safety Minister Anne McLellan.
The federal budget said last week it was spending $605 million for increased security at marine ports, better threat assessment, and intelligence and fingerprint analysis.
And last week, McLellan announced a project to create a communications system to help federal agencies share information.
Tuesday's report also examined areas such as the regulation of medical equipment, the black market economy and new mechanisms put in place since Paul Martin became prime minister to curb government spending abuses.
Opposition members of Parliament were quick to jump on the security portions of the report, however, hammering the government during question period on the problems found there.
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