The opposition parties hammered the prime minister in question period Tuesday over the Senate expense scandal, demanding to know why Stephen Harper’s chief of staff remained on the job for five days after he learned of the $90,000 cheque he wrote to help Sen. Mike Duffy repay ineligible expense claims.

Tuesday marked the first day the opposition was able to ask Harper about the cheque since it was first reported by CTV News, as the prime minister was away the previous week on a trade mission to Latin America.

Under questioning from NDP Leader Thomas Mulcair, Harper first said that he only learned of the cheque via news reports on May 15, and then later said he heard about the cheque from Wright himself on that date.

Under questioning from Liberal Leader Justin Trudeau, Harper said that he had assumed Duffy had repaid the money himself until he was informed otherwise by Wright.

“The prime minister has repeatedly stated in this House today that he only learned about the deal between Mr. Wright and Mr. Duffy on the 15th,” Trudeau said.

“However, on the evening of the 14th CTV News ran the story about this deal, and included commentary from the prime minister’s own office that no taxpayer money was used. Is the PM not aware so completely about what’s going on in his own office that he didn’t know the night before when the news broke?”

“I think I’ve been very clear that until the morning of the 15th when Mr. Wright informed me that he had written a personal cheque to Mr. Duffy so that he could repay his expenses, it had been my understanding that Mr. Duffy had paid from his own personal resources,” Harper replied.

Trudeau then noted that it was five days later, the following Sunday, that Wright stepped down from his post.

“If the PM learned about the $90,000 payment at the same time as the rest of us, why did it take him a week to relieve his chief of staff of his responsibilities?” Trudeau asked.

“By his own admission, Mr. Wright made a very serious error,” Harper replied. “For that he has accepted full, sole responsibility. He has agreed to resign and he is subject to an investigation, an examination by the ethics commissioner, on which I anticipate he will be fully co-operative.”

Earlier Tuesday, Wright told CTV News that he made mistakes, but can stand behind everything he did.

Wright has kept a low profile since he resigned on May 19 after CTV News revealed he had written a personal cheque to cover $90,172 in invalid expense claims owed by Duffy.

Wright resigned amid the growing scandal, saying in a statement that he believed repaying the funds that Duffy had improperly claimed was "in the public interest."

CTV's Daniele Hamamdjian interrupted Wright as he went for a run around 4 a.m. Tuesday morning.

"I'm going to first of all give my submissions to the ethics commissioner, she's going to look into this and I think I can stand behind everything I did," Wright said Tuesday after stopping to answer question from CTV’s Daniele Hamamdjian.

"I made some mistakes, I'm living with the consequences of those mistakes, but I believe I can account for my actions and I think that's the right forum for it."

Ethics Commissioner Mary Dawson has confirmed her office has launched an investigation into Wright's cheque to Duffy under the Conflict of Interest Act.

Duffy quit the Conservative caucus following the controversy, though he is still a senator and has said he believes he will eventually be exonerated.

After Duffy said he was repaying the debt, the Conservatives praised the senator for showing "leadership," and suggested other senators should follow his example.

Harper has said he was not aware Wright planned to cut a cheque to Duffy and was upset when he learned what had taken place.

"I don't think any of you will be very surprised to hear I'm not happy, I'm very upset, about the conduct we've witnessed, the conduct of some parliamentarians and the conduct of my own office," Harper said, responding to the controversy during last week’s trip.

On Tuesday Mulcair asked short, pointed questions about many of the allegations that have surfaced throughout the affair.

After asking repeatedly when the prime minister knew of the $90,000 cheque, Mulcair asked Harper if he ordered Wright “or other members of his office to resolve the problems with spending by Sen. Mike Duffy.”

Harper responded that he “didn’t give directives,” and his view was that Duffy had repaid the money out of his own pocket until he learned otherwise on May 15.

Trudeau asked if Harper would release “all records -- emails, documents, correspondence and other -- relating to any arrangement between Mr. Wright and Mr. Duffy.”

Harper responded that the issue is now before “the ethics commissioners in each chamber of this Parliament, and obviously should we be asked to produce any kind of information we would be happy to do so.”

Harper also said he had never discussed the issue with his cabinet, saying “it is not a matter of government or cabinet business. That is plainly obvious.”

CTV News has reported that Harper’s former special counsel and legal adviser Benjamin Perrin worked on a deal between Wright and Duffy’s lawyer to help the senator pay back the invalid expense claims.

The Prime Minister's Office has issued a statement that Harper was not informed of the payment to Duffy, or about any aspects of a secret arrangement.

And in an email to CTV News, Perrin said he was "not consulted on, and did not participate in, Nigel Wright's decision to write a personal cheque to reimburse Senator Duffy's expenses."

Perrin noted he has never communicated with Harper about the subject. He has not denied working on the secret arrangement with Duffy's lawyer.

On Tuesday, Harper responded to a question about Perrin’s involvement in the deal by saying Perrin “has already answered those questions,” after earlier maintaining that “to my knowledge, there is no legal agreement between (Wright and Duffy).”

Mulcair also asked if he had seen the cheque and if he would produce a copy. Harper replied that “there is no cheque from the Prime Minister’s Office. There is no use of prime minister’s office funds in this affair. This was an action Mr. Wright took using his own resources on which he is now subject to examination and accountability by the ethics commissioner.”