Prime Minister Stephen Harper defended his decision not to accept the resignation of his natural resources minister on Wednesday after it was revealed documents related to Canada's nuclear industry were left behind at an Ottawa news bureau for almost a week without anyone in the government noticing.

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Natural Resources Minister Lisa Raitt, left, and her press secretary, Jasmine MacDonnell, are seen leaving a news conference in Ottawa last month. ((Fred Chartrand/Canadian Press))

The prime minister told Natural Resources Minister Lisa Raitt she could keep her job, while the resignation of a member of her staff was accepted.

Speaking to reporters in Quebec City, Harper said the breach was a "serious matter" and added, "There should be changes." 

But he said he believes the breach was not a result of the minister's "personal action," as was the case in Harper's decision last year to accept the resignation of former foreign affairs minister Maxime Bernier over his misplacing confidential government documents.

Raitt, Harper said, "was undertaking employment activity, ministerial activity in the company of her staff who were responsible for these documents and certainly for accounting for these documents later."

"I think she had a reasonable expectation that that would be done," he said.

The prime minister was not in the House of Commons during Wednesday's question period, leaving Raitt to fend off heated queries from Opposition MPs over her competence.

After receiving a standing ovation from Conservative colleagues as she rose to speak, Raitt admitted "clear procedures were not followed in this case."

She told the House she offered to resign, but Harper refused to accept it. She said she had accepted the resignation of her aide.

"Corrective action has been taken," said Raitt, amid calls of "scapegoat" and "unbelievable" from Opposition MPs.

"I offered to resign if the prime minister felt it necessary. He did not accept it. The person responsible for handling the documents offered their resignation, and I did accept it."

The Conservatives declined to identify the aide, but media reports quoted Raitt's 26-year-old press secretary, Jasmine MacDonnell, as saying she had resigned.

Liberal Leader Michael Ignatieff called the minister's allowance of a staffer to take the blame "despicable," telling the House the blunder speaks to the issue of "competence in relation to the whole government."

"It's presumably the same staffer responsible for the isotope shortage and it's presumably this 26-year-old who is responsible for the whole darned department," Ignatieff said.

"How are we supposed to believe such a fiction?"

Bloc Québécois Leader Gilles Duceppe and New Democrat MP Thomas Mulcair accused the government of forcing the subordinate to carry the blame for the minister's incompetence.

Mulcair cited Harper's own words a year ago following the Bernier affair that ministers were personally responsible for the handling of sensitive documents in their departments.

Bernier resigned as foreign affairs minister last year after he admitted to having left NATO briefing documents at his ex-girlfriend's home.

"The rules say that she is responsible, not some underling," Mulcair told the House, pointing to the minister. "How come a year ago, the minister had to resign and today they're allowed to blame an underling, a subservient person, for all the responsibility of the minister?"

In a rare deviation from her much-repeated statement to the House, Raitt replied she was concerned about the language and tone of Mulcair's question, saying it indicated "maybe perhaps only a woman could be subservient."

The New Democrat MP angrily dismissed Raitt's claim as "pure, unmitigated nonsense."

Documents show $71M more earmarked for AECL

The documents, which were marked "secret," were left at CTV's Ottawa news bureau about a week ago, CTV reported earlier Wednesday.

The materials include handwritten notes, information regarding Conservative government strategy, background documents and reports regarding Atomic Energy of Canada Ltd.'s Candu division in an internal briefing binder, said CTV.

According to a report among the documents, the federal government has provided AECL with $1.7 billion in funding since 2006. A talking-point memo describes the spending as "cleaning up a Liberal mess."

The 2009-10 federal budget shows that $351 million was earmarked for the Crown corporation but the documents indicate that $72 million aimed at "maintaining the option of isotope production" not previously stated publicly will also be given to AECL this year, CTV said.

"The additional $72 million that appears in this document — I'm not aware of any mention of that anywhere else," said Liberal natural resources critic Geoff Regan.

"When you consider that over the past two years the government has put $1.7 billion into Chalk River and still can't guarantee the supply of isotopes for Canadians — it's disturbing," he said.

Documents retrieved after a week

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An unidentified government official picks up the documents at the CTV office in Ottawa. ((CBC))

No one from the minister's office called the network to inquire about the missing documents until CTV's possession of them was widely reported on Wednesday, the network said. The minister's office sent a staff member over to retrieve the binder on Wednesday.

Regan said "it's very disturbing" that Raitt and her staff either didn't realize or refused to admit they'd left behind the documents.

"Surely the responsibility of the government is to track these things down quickly," he said.

A review into the Bernier affair last year recommended a range of measures to beef up ministerial security, including better training, stricter monitoring and improved measures to track briefing books.

Harper on Wednesday said he believes Bernier has "learned a lot" from his experience and will continue to be an "important part" of the Conservative team.

'Sensitive' material

Officials in the minister's office have told the CBC that though many of the documents contained in the binder were stamped secret, the material is actually just "sensitive" in nature.

Raitt announced last Thursday the federal government may sell a stake in AECL's commercial reactor division to strengthen the business as part of a restructuring process.

The company's research-and-development division, Chalk River Laboratories, will continue to be government-owned but with private-sector management, she said.

The Chalk River nuclear reactor, which provides about a third of the world's medical isotopes, is currently on a shutdown expected to last for three months due to a heavy water leak.

AECL has already run out of medical isotopes and doctors are scrambling to collect a scarce supply from the world's four other isotope-producing reactors.

The documents left at CTV also indicate that AECL is looking at about $100 million in cost overruns this year related to its refurbishment of Ontario's Bruce Power reactors and costs at its Candu reactors around the world, CTV said.

The paperwork also shows the refurbishment of the reactors is up to 433 days behind schedule.

With files from The Canadian Press