The federal government needs to do better at tracking and evaluating some of its program spending to ensure taxpayer dollars are being well-spent, Auditor General Michael Ferguson found in his spring report released today, and one of the most striking examples is that it can't account for $3.1 billion in anti-terrorism funding.

The lack of information on spending and on results achieved for money spent is a common theme throughout Ferguson's report, which includes 11 chapters in total.

In his audit of the Public Security and Anti-Terrorism (PSAT) Initiative Ferguson suggested there should have been a government-wide review of spending and results for the program that was funded between 2001 and 2009.

He found that departments reported spending $9.8 billion of the $12.9 billion allocated for security and anti-terrorism measures under the program but he couldn't determine where the other $3.1 billion went. The Treasury Board had no clear answers for him.

Ferguson said he's not concerned the money is missing, it's the information about it that can't be nailed down.

"It's a matter of missing that last link in putting that information together," he said at a news conference in Ottawa Tuesday morning. If the money was reallocated from the anti-terrorism program to another program, there should have been approval for that, he added.

"We don’t have enough information to say whether that happened," he said.

The NDP jumped on the accounting gap as a sign the Conservatives can't manage the public purse.

"It is really scandalous that [the government] can't account for the $3.1 billion," NDP MP Malcolm Allen said.

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Treasury Board president Tony Clement said there are no allegations of misspent or misallocated money and that Parliament was "in the loop" on how money was spent.

"All government spending, every nickel and dime is reported to Parliament and accounted for each and every year in the public accounts," he said.

Clement said he accepts the auditor general's recommendation for his department to provide a clear picture of spending and results for government-wide programs.

Some of the other main findings in the report include:

Some departments, including National Defence, aren't always doing proper security clearances for people and companies hired on contract.

The Truth and Reconciliation Commission and the government are not acting in a spirit of reconciliation to create a complete historical record of the residential school system, and there is no plan on how to resolve their disputes.

The Public Health Agency of Canada is doing a poor job of managing the Canadian Diabetes Strategy and the impact of the program is unknown.

The Canada Revenue Agency is doing better at collecting unpaid taxes, but needs to do more given there are arrears of $29 billion.

Better reporting on how development aid money is spent and what results are being achieved is needed.

There are concerns over the sustainability of search and rescue activities because of aging equipment and personnel shortages.

Human Resources and Skills Development Canada (HRSDC) is doing better at cutting down employment insurance overpayments, but still losing millions a year.

Ferguson's report on anti-terrorism spending comes at a time when the subject is dominating public debate and Parliament Hill. Anti-terrorism measures were debated in the House of Commons last week, on the same day that arrests were announced by the RCMP. A man from Toronto and another man from Montreal are accused of plotting a terrorist attack on a Via passenger train.

Safety and security were also raised in other chapters of Ferguson's report. He found that some departments, including National Defence, are not following proper procedures for security clearances when outside people or companies are hired on contract. In some cases people were awarded contracts who did not have appropriate security clearances.

Defence Minister Peter MacKay's department is also singled out in the spring report for its management of search and rescue (SAR) activities. Ferguson said he has concerns about the sustainability of SAR activities because of aging equipment and personnel shortages.

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