The Opposition Liberals levelled allegations of a cover-up in the Maxime Bernier affair Wednesday, accusing the Conservative government of sitting on a "national security bomb."

Liberal Deputy Leader Michael Ignatieff said on CTV Newsnet's Mike Duffy Live that the timeline of events the Tories have given about the scandal over the misplaced classified documents doesn't make sense.

"We're talking cover-up here. The opposition simply does not believe the government's story," Ignatieff said.

The strongly-worded accusation came just hours after Liberal MP Ujjal Dosanjh suggested in question period that the Prime Minister's Office may have known about the missing documents well before Bernier's resignation on Monday.

Bernier resigned his post as foreign affairs minister after informing Prime Minister Stephen Harper that he had left classified documents at the home of an acquaintance. His ex-girlfriend, Julie Couillard, returned the documents to the government this past weekend -- apparently several weeks after they went missing.

Timeline questions

The Tories have insisted that Harper only learned of the missing documents when Bernier tendered his resignation. The Liberals say the Conservatives' timeline of events is raising questions.

"Can the public safety minister confirm that between May 1st and May 8th of this year there was a meeting of CSIS and the Prime Minister's Office to discuss the conduct of his foreign affairs minister," Dosanjh asked in the Commons Wednesday.

In the Commons, Public Safety Minister Stockwell Day said discussion of meetings between CSIS and the PMO were not a matter of public record. Dosanjh said later that "we didn't get a denial" regarding the premise of the question.

Day's office sent an email to CTV on Wednesday evening saying the meeting did not take place. The email quoted Day as saying that "The Opposition is just making wild allegations."

On Mike Duffy Live, Conservative MP Jason Kenney repeated the Tories' admission that Bernier made a "serious mistake." Kenney noted that the prime minister only learned of the missing documents "two days ago."

Ignatieff said "the idea that these documents floated around for three, four, five weeks without anybody realizing they were in Julie Couillard's apartment defies credibility."

Commons debate

The Tory scandal had earlier dominated question period in the House of Commons.

Accusing the Conservative government of giving Canada an "international black eye," the Liberal opposition called on the Tories to ask the Mounties to conduct an independent investigation into the scandal.

The Conservatives said that foreign affairs will conduct an internal investigation -- and department officials will call for outside help should it be required.

But the Liberal, NDP, and Bloc Quebecois MPs accused the Tories of ducking a thorough investigation. They demanded to know how wide-ranging the security lapses may have been.

"Have national secrets been forgotten at Starbucks or the gym," asked NDP Leader Jack Layton.

Dosanjh had said in the Commons that the RCMP should investigate, and added that another independent body also needs to look into the matter.

Also on Wednesday, Bernier released a statement saying he will stay in the Commons.

In the statement he took full responsibility for the events that led to his resignation. He also said he would continue to serve as an MP and "will perform my functions (as a) Member of Parliament for (the Quebec riding of) Beauce with commitment, conviction and integrity."

He wrote in his statement, "I also express regret over the negative impact caused by recent events on Ms. Couillard's private life."

Ignatieff said in the Commons the scandal has made Canada a "laughing stock" in the international community.