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Prime Minister Stephen Harper said he let Minister of Natural Resources Lisa Raitt keep her job because her staff was responsible for the secret documents left behind at Â鶹´«Ã½' Ottawa bureau.

Harper said because Raitt was "working at the time" when the documents were misplaced, the case was different than the one involving former foreign affairs minister Maxime Bernier, who had to resign after misplacing classified documents.

"In the case of Mr. Bernier, his actions were much more personal and that was the difference in responsibility," Harper told reporters Wednesday afternoon.

"(Raitt) was undertaking ministerial activity in the company of her staff, who were responsible for these documents, certainly for accounting for these documents later . . . and she had a reasonable expectation that that would be done."

The documents were left behind for nearly a week without any inquiry from Raitt's office. A staffer has resigned over the matter.

Harper said that the incident was "a serious matter and there will have to be changes."

Raitt told the House of Commons during question period that she offered her resignation to Prime Minister Stephen Harper Wednesday.

"Certain procedures were not followed in this case. Corrective action has been taken. I offered to resign if the prime minister felt it necessary. He did not accept it," she said.

"The procedures in place were clearly not followed. Corrective action has been taken. And I have accepted the resignation of the individual who is responsible for the documents."

The staffer is Jasmine MacDonnell, 26, Raitt's director of communications. "I offered my resignation," she said Wednesday, as she left the prime minister's offices on Parliament Hill. MacDonnell also served as press secretary to former natural resources minister Gary Lunn.

Kory Teneycke, a spokesman for Harper, told Â鶹´«Ã½ Channel's Power Play that there were two failures in security procedures.

The first was leaving the documents behind, and the second was that the documents were not reported missing.

There was supposed to be an overhaul of classified document security after the Bernier affair, and Teneycke admitted the new system has failed.

"It has been tightened up . . . but obviously this is a failure of that system to work properly," he said.

Teneycke said that ultimately the staffer was individually responsible for the secret documents and would only say the "government is globally responsible" for the system's failure in this case.

A wrinkle in the official explanation is the difference between who signed out the document, who was using it and who was ultimately responsible for its security.

"Sources have told CTV that that briefing document actually was the minister's document," CTV Ottawa Bureau Chief Robert Fife said Wednesday. "Why did the minister not ask, 'where is my briefing document, why is it missing?'"

The documents also featured Raitt's own handwriting on them. Raitt did not learn they were missing until CTV reported on the documents Tuesday night.

Opposition demands Raitt resign

The opposition parties demanded that Raitt resign and said that she is ultimately responsible for mistakes made within her department.

"The issue here is an issue of competence and not just competence in relation to this minister but competence in relation to the whole government," Liberal Leader Michael Ignatieff said.

"Canadians want competence in their government, when are they going to get it?"

Last May, Bernier resigned from his post as foreign affairs minister after acknowledging he had left behind classified government documents at the home of his former girlfriend Julie Couillard.

"Ministers are always responsible for the protection of classified documents," Harper said in the House of Commons on June 2, 2008.

"The minister admitted that he failed to protect classified documents. That is why he offered his resignation and why I accepted it."

NDP MP Thomas Mulcair said the prime minister is not following his own rules in the case of Raitt.

"The rules say that she is the one responsible, not some underling. How is that acceptable?" he asked during question period. "It's unacceptable. She should resign and leave immediately."

Harper was not in the House to answer questions on the matter.

On Wednesday, a federal government employee picked up the documents after CTV reported Tuesday night that they had been left behind for six days.

The documents reveal Ottawa has poured far more money into the aging Chalk River nuclear reactor than the public has been told.

Some of the papers are clearly marked "secret."

CTV's Graham Richardson said nobody from Raitt's office called to ask for the documents since they went missing.

"If they weren't noticed missing, why is that? And if they knew they were missing why didn't they call around?" Richardson questioned on Wednesday.

"Did they not call around because they didn't want to alert the media that they had lost some documents? Did they not know where they'd lost them?"

Details of the documents

Ontario's Chalk River reactor supplies at least one-third of the world's medical isotopes, which are used in diagnostic tests for some forms of cancer. Atomic Energy of Canada Ltd. shut down the reactor last month because of a heavy water leak.

In documents headlined "Background for discussion with chair of Atomic Energy Canada," the government lists funding for the Crown corporation at $351 million for 2009-2010. That figure was in the January budget.

However, it also lists $72 million to "maintain the option of isotope production." The public 2009 budget does not specifically mention funding for isotopes.

The documents also include a hand-written note that lists total funding for Atomic Energy of Canada, Ltd. since 2006 at $1.7 billion, and then a talking-point memo to characterize the spending as "cleaning up a Liberal mess."

The Conservative government plans to privatize AECL's nuclear reactor division in order to boost sales of its CANDU reactors, as Ontario weighs whether to buy two new power plants.

Publicly, Ottawa has downplayed Ontario's interest in the sale of AECL's Candu division. But included in the binder is background information for a May 25 meeting with Glenna Carr, who chairs the board of directors for AECL: "The government continues to support AECL's bid in Ontario, but the announcement will probably raise questions about this support. We will have to manage this very carefully."

Other documents highlight cost increases for AECL that have not been made public. In one document headlined "Discussion with CEO Hugh MacDiarmid, CEO of Atomic Energy Canada," it lists $100 million in supplementary funding to keep it solvent.

That figure includes cost increases to refurbishing Ontario's Bruce Power reactors and cost-overruns at Candu reactors around the world, according to the documents.