The prime minister has maintained that he was kept in the dark by his former chief of staff, whom he said acted alone in organizing the controversial deal. Harper said he only learned about the cheque from news reports on May 15.
But Duffy told his Senate colleagues Tuesday that the arrangement was part of a larger "conspiracy" to quickly snuff out controversy over his Senate expenses because Harper wanted to appease his Tory base.
Listen to Duffy's Senate speech
Duffy's allegations sent Ottawa into a tailspin this week but the PM's spokesperson, Jason MacDonald, issued a release Tuesday saying there was nothing new in Duffy's speech.
"It's on the public record. Following a caucus meeting Mr. Duffy approached the prime minister and raised his expenses. The prime minister made it clear that any inappropriate expenses should be repaid. That's it. That is the only time the prime minister discussed Mr. Duffy's expenses with him."
But there are still many things Duffy said that could complicate things for Harper -- here are six reasons why:
1. Harper says he didn't talk about Duffy to anyone for three months
As pointed out by the CBC's Chris Hall on Wednesday, Harper has stated that a February meeting with Duffy was the last time he talked to anyone about the matter until the news broke about the deal on May 15.
"That's three months without showing any interest in whether Duffy had followed his orders, or inquired about what had been done to close the matter," Hall wrote.
2. A 'slew' of Harper staffers apparently knew about the payment
RCMP documents confirm others in the PMO were aware of the Duffy deal.
From an editorial in the Toronto Star:
While Wright may initially have acted alone, the RCMP reports that a slew of people in the PMO knew of the payment. Wright recalls telling three others about it: Benjamin Perrin, a lawyer; Chris Woodcock, director of issues management; and David van Hemmen, Wright’s assistant. He also told Sen. Irving Gerstein, chair of the Conservative Fund Canada, the party’s fundraising arm. At some point this reached deep into the PMO and the party.
3. Nigel Wright kept a binder on Duffy
RCMP documents filed in court this month show Harper's top staffer kept close tabs on Duffy's official and personal activities while the former Tory senator's expenses were under the microscope. In fact, Wright had a binder of calendars with detailed notes on the senator's travel, meetings, social events, speeches and interactions.
But a PMO spokesperson maintains the Duffy file was "handled by Nigel Wright and he has taken sole responsibility."
4. Harper didn't demand Wright’s resignation right away
On May 16, a day after news of the deal broke, Harper's director of communications said Wright had "the full support of the prime minister."
On May 19, Harper accepted the resignation of his former right-hand man.
When asked about the delay in June, Harper conceded he perhaps should have responded quicker.
"He should have told me earlier; that's why I accepted his resignation," Harper told reporters. "Upon reflection, should I have reached that conclusion earlier? Perhaps."
5. Harper dodged questions about the first time he discussed Duffy's expenses with Wright
The following is from question period that took place on May 28.
Mulcair: Mr. Speaker, on what date and at what time was the prime minister informed that Nigel Wright had made a payment to Conservative Senator Mike Duffy?
Harper: Mr. Speaker, I have been very clear on this question. This matter came to my attention two weeks ago, after speculation appeared in the media.
On Wednesday, May 15, I was told about it. At that very moment, I demanded that my office ensure that the public was informed, and it was informed appropriately.
Mulcair: Mr. Speaker, when did the prime minister first speak with Nigel Wright about Mike Duffy's expenses?
Harper: Mr. Speaker, as I have said repeatedly, my first knowledge of this was on the date and at the time indicated.
Prior to that point in time, it was my understanding that Mr. Duffy had paid back his own expenses.
Mulcair: Mr. Speaker, the question was when did the prime minister first speak with Nigel Wright about Mike Duffy's expenses, and how many times did he speak with Nigel Wright in the week preceding his resignation?
Harper: Mr. Speaker, if the leader of the NDP is suggesting I had any information to the contrary from Mr. Wright prior to this, that is completely false. I learned of this on May 15 and immediately made this information public, as I have said many times.
Mulcair: Mr. Speaker, we are asking very simple, straightforward questions and the Prime Minister is not answering them. That is the problem. Canadians want answers.
What instructions did the prime minister give to Nigel Wright or other people in his office to solve the problem of Conservative Senator Mike Duffy's expenses?
Harper: Mr. Speaker, I did not give any such instructions. It was my opinion that Mr. Duffy was to pay his own expenses, and that is what I believed until May 15.
6. Harper and Duffy disagree on whether Ray Novak was involved
On June 5, Mulcair asked Harper directly in question period if his new chief of staff was played a role in the Duffy deal.
"Was Ray Novak involved in any way, shape or form in these discussions concerning Mike Duffy, yes or no?" Mulcair wondered.
According to a French-to-English translation, Harper replied:
"Mr. Wright decided to take an action on his own initiative, using his own funds. These actions are his sole responsibility. I have no information before me to suggest they are anyone else's responsibility. Mr. Wright is obviously answering for those actions, which he admits were a mistake, to the appropriate authorities."
But Duffy claimed Tuesday that Novak was absolutely involved in his discussions with Harper's office.
"I was called at home in Cavendish by Ray Novak, senior assistant to the Prime Minister. He had with him Senator LeBreton, Leader of the Government in the Senate,” Duffy said. “Senator LeBreton was emphatic: The deal was off. If I didn't resign from the Conservative caucus within 90 minutes, I'd be thrown out of the caucus immediately, without a meeting, without a vote."
Mulcair again asked Harper about Novak during question period Wednesday.
"On June 5 and 6, when I asked the prime minister whether Ray Novak was involved in the Duffy affair, the prime minister said that Nigel Wright acted alone. Was that true?" Mulcair wondered.
"Mr. Wright has been absolutely clear in terms of who he told he intended to repay Mr. Duffy's expenses to. He did not say Ray Novak was one of those people. He has named those people. He has been very clear," Harper said. "He has also been very clear that one of those people was not me because I obviously would never have approved such a scheme."
With files from The Canadian Press
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