Canada's Auditor General raised red flags around food safety, border security, emergency plans in First Nations communities living on reserves and rail safety in his annual fall report tabled on Tuesday.

Michael Ferguson said even when the federal government identified a problem, it took too long to come up with and implement solutions.

"The resulting delays can have significant impact on Canadians both directly and indirectly," Ferguson said on Tuesday after he tabled his report in the Commons.

"A look over the audits we are reporting on today show that in many cases, the results need to be improved," Ferguson said.

The auditor general found, for instance, that the Canadian Food Inspection Agency did recall unsafe food products in a timely fashion, but the recall system fell apart once a major food recall was announced.

"While illnesses were contained in the recalls we examined, I am not confident that the system will always yield similar results," Ferguson said.

The CFIA did not adequately manage the food recall system between 2010 and 2012 said Ferguson, who found that the agency did not have the documentation necessary to determine whether recalled food products had been disposed of, nor did it have the information necessary to identify and correct the cause of the recall in a timely way.

While registered meat establishments are required to maintain product distribution records to quickly help locate products during a food safety investigation, the audit report found many examples of incomplete documentation.

The auditor general also found:

The federal government will need to keep an eye on costs for its national shipbuilding procurement strategy to ensure Canada gets the ships and capabilities it needs to protect its national interests and sovereignty.

Responsibility for emergency management in First Nations communities living on reserves among the various stakeholders was either absent or unclear.

Producers impacted by disasters with smaller total payouts often wait more than a year to receive financial help.

Accessing government services online is complex, requiring multiple steps . A retired veteran, for example, would have to navigate back and forth between three or four departments just to manage their benefits or taxes online, the auditor general said.

. A retired veteran, for example, would have to navigate back and forth between three or four departments just to manage their benefits or taxes online, the auditor general said. Five of seven audited departments and the Treasury Board made unsatisfactory progress in their efforts to ensure that effective internal controls over financial reporting were in place since recommendations made by the auditor general in 2011.

The Canada Revenue Agency did a good job of following-up on the information it received about offshore accounts.

On the subject of food safety, the auditor general looked at two large meat recalls in 2012, and found that timely access to records was a challenge.

The XL Foods investigation was delayed because the firm was slow in providing the CFIA with distribution records, which the agency said were given to them in an unusable format. The investigators spent several days going through the paper work before it could be used.

Similarly, the recall by New Food Classics in March 2012 also involved delays in obtaining distribution records, the audit report found.

Five federal ministers held a press conference in Ottawa following the auditor general's report to say they have accepted all of Ferguson's findings and have begun to implement his recommendations. Health Minister Rona Ambrose reacts to Auditor General Michael Ferguson's latest report at a news conference in Ottawa, Tuesday, Nov. 26, 2013 as fellow ministers (left to right) Tony Clement, Diane Finley, Lisa Raitt and Steven Blaney look on. (Sean Kilpatrick/Canadian Press)

Health Minister Rona Ambrose said while her department will have completed all of the auditor general's recommendations by the spring, she called the problems identified in the audit report largely "administrative."

Those administrative recommendations "don't imply any food safety risks to the public," Ambrose said.

But New Democrat MP Malcolm Allen said the gaps identified by the auditor general in "the flow of information and the cohesiveness of the system" could actually have an impact on the time it takes the government to issue a food recall.

Allen said the auditor general's findings are "an indictment" of the federal government's overall mismanagement.

Quarter of railway audits completed

The auditor general was also concerned with "significant weaknesses" found in Transport Canada's oversight of rail safety.

Transport Canada completed only one in four of its planned audits of federal railways over a three-year period, due in part to a lack of inspectors, the audit report found.

While Transport Canada made progress in addressing many of the recommendations from the Railway Safety Act review, the audit report found that a number of long-standing and important safety issues remain.

There were issues of "trespassing, grade crossings, concerns about the environment, the collection of data on safety performance from federal railways, and the implementation and oversight of safety management systems," the report found.

Transport Minister Lisa Raitt told reporters gathered in Ottawa that her department has developed "an accelerated plan" to respond to all of the auditor general's findings.

She said the federal government has taken "strong action" to increase rail safety and the transportation of dangerous goods across the country in the last six months — a period which includes the tragic train derailment in Lac-Mégantic last July.

Raitt also noted there were 30,000 inspections of federal railways last year, the highest number ever, she said.

The transport minister announced last week that the federal government will require railway companies to inform the communities their trains run through of the dangerous goods they are carrying, following the auditor general's preliminary findings and ahead of this week's report.

NDP MP Allen called the lack of federal railways audits "a serious problem" that needs to be addressed immediately.

Too many border controls 'not working'

Another major concern identified by the auditor general in his fall report had to do with illegal entries into Canada.

People who pose a risk to the safety and security of Canadians have succeeded in entering the country illegally, the auditor general found.

"I am very concerned that our audit found too many examples of controls not working," Ferguson said.

The Canada Border Services Agency does not always receive the information it needs from air carriers in order to efficiently target high-risk passengers, the audit report found.

It also said, the RCMP often lacks the information necessary to monitor the success of its border enforcement activities.

Public Safety Minister Steven Blaney told reporters in Ottawa his department will work with the CBSA and the RCMP to see how they can improve the exchange of information.

The federal government has issued a statement for each of the audits contained in the fall report of the auditor general outlining what action it is taking.