The Prime Minister's chief of staff has resigned in the midst of the most serious scandal to hit Stephen Harper in his seven years in office.

Nigel Wright announced his resignation Sunday morning, just days after CTV Ottawa bureau chief Robert Fife reported that he wrote a personal cheque to help Senator Mike Duffy pay back more than $90,000 in improperly claimed senate living expenses.

Wright said he believed repaying the funds that Duffy had improperly claimed was “in the public interest,” and said he accepts sole responsibility in the matter.

"My actions were intended solely to secure the repayment of funds, which I considered to be in the public interest, and I accept sole responsibility," Wright said in a statement. "I did not advise the Prime Minister of the means by which Sen. Duffy's expenses were repaid, either before or after the fact.

Harper said in a statement that he accepted Wright’s resignation with “great regret” and thanked his top aide for his contributions to the Tory government.

“I accept that Nigel believed he was acting in the public interest, but I understand the decision he has taken to resign. I want to thank Nigel for his tremendous contribution to our government over the past two and a half years.”

Ray Novak, who has served as Harper’s principal secretary since 2008, is taking over as the prime minister’s chief of staff.

On Thursday, Duffy announced he quit the Conservative caucus and would sit as an Independent, as the public controversy surrounding the repayment of Senate expenses had become a “distraction.”

Following news of Wright’s resignation, NDP ethics critic Charlie Angus said the Harper government is in “full-fledged panic mode.”

"Why, for months, was Sen. Duffy allowed to pretend he paid the money out of his own pocket,"Angus said on CTV Question Period Sunday.

Liberal MPs were also quick to indicate that the controversy is far over, and when parliament resumes on Tuesday after a break, questions are likely to dog the Conservatives.

Foreign affairs critic Bob Rae said he was not surprised by Wright’s resignation and stressed the need for an independent investigation into the matter.

“If the Conservatives are not prepared to let it go to a parliamentary committee, then they need to appoint a special investigator or someone who has the capacity to ask all the difficult questions,” he said Sunday afternoon.

Rae added that the scandal has more to do with the Prime Minister than the Senate itself.

“This is about Mr. Harper. This is about the Prime Minister’s Office, how the Prime Minister’s Office operates and the ethical and legal standards by which it operates,” he said. “That’s where the focus is, and that’s where it now belongs.”

Calls for investigations

Last week, the New Democrats asked Senate Ethics Officer Lyse Ricard to launch an investigation in the matter, claiming the $90,000 cheque from Wright violated ethics rules that prohibit senators from accepting gifts.

Under the Senate Conflict of Interest Code, all gifts over $500 must be reported within 30 days.

“What people need to know about the Senate is it’s such an old boy’s club that you actually need the permission of the Senate to begin an investigation,” Angus said.

Duffy’s expenses had been the subject of an internal audit, along with those of Senators Patrick Brazeau and Mac Harb.

Under the Senate’s housing rule allowance, senators can be compensated for living expenses if they live more than 100 kilometres from Ottawa, requiring them to maintain a secondary residence.

However, according to evidence outlined in an independent audit showed that Duffy, Brazeau and Harb each spent more time in the capital than at the homes declared to be their primary residences, rendering their claims ineligible.

Earlier this month, a Senate committee ordered Brazeau to repay about $48,000, and Harb $51,000.

Brazeau insists that he didn’t break rules by claiming the housing allowance, and he is determining if the order to repay the money can be overturned. Harb has retained a lawyer and will attempt to “quash” the audit’s findings.

On Tuesday morning, Harper will hold an emergency meeting with Conservative senators and MPs, many overwhelmed by complaints they've been hearing from their constituents about the issues raised in recent weeks.