Prime Minister Stephen Harper's chief of staff Nigel Wright personally bailed out Mike Duffy by writing a cheque to the Conservative senator that was used to repay more than $90,000 in improperly claimed Senate living expenses.

The Prime Minister’s Office confirmed Wednesday to CTV’s Ottawa Bureau Chief Robert Fife that Wright, a former Bay Street executive, gave Duffy a cheque from his personal bank account for the full amount owing: a total of  $90,172.

"Mr. Duffy agreed to repay the expenses because it was the right thing to do. However, Mr. Duffy was unable to make a timely repayment," Harper’s director of communications Andrew MacDougall wrote in an email.

"Mr. Wright therefore wrote a cheque from his personal account for the full amount owing so that Mr. Duffy could repay the outstanding amount."

That confirmation from the PMO contradicts Duffy’s own explanation to CTV News Tuesday night.

In an email, Duffy claimed that he got a loan to repay his expense claims. 

“The Royal Bank helped me…I dealt with my bank personally. Nigel played no role,” he wrote.

On Tuesday, Fife reported that Wright had secretly intervened to help Duffy pay back the money he owed for the improperly claimed expenses while an external audit was still underway.

Sources said the deal involved Duffy reimbursing taxpayers in return for financial help and a promise from the government to go easy on him.

In a Feb. 20 email, Duffy said Wright worked out a “scenario” in which all of his claimed living expenses would be covered, including “cash for the repayment.”

Two days later, Duffy publicly vowed to reimburse the taxpayers, saying he "may have been mistaken" when he filled out Senate housing allowance forms, claiming a cottage in Prince Edward Island as his primary residence.

Wright has been the prime minister’s chief of staff since 2011. The $90,000 cheque is a personal gift from Wright to Duffy, but insiders say the two men are not close friends and hardly know each other.

The PMO said Harper had no knowledge of the transaction, but NDP MP Paul Dewar said he doesn’t believe that.

“I believe he had to know something,” he said.

A senior PMO official told Fife that Duffy couldn’t afford to repay the $90,000 and did not want to borrow money from a bank, fearing that his wife would be stuck with the large debt if he died suddenly from a heart attack. Duffy has battled cardiac problems over the years.

The NDP is calling for an independent inquiry into the Senate expense scandal and the ethics of Wright’s involvement.

“We spend our time making lists of baseball caps and books that we receive as we tour the country and submitting those to avoid any appearance of conflict on an ethics level,” Opposition Leader Thomas Mulcair said Wednesday.

“So how someone who’s a sitting senator can expect $90,000 to get him off the hook…is part of the answer that we’re still looking for.”

The Senate Conflict of Interest Code requires Senators to disclose all gifts over $500 within 30 days of receipt.

The code also includes a general statement on gifts that says “neither a Senator, nor a family member, shall accept, directly or indirectly, any gift or other benefit, except compensation authorized by law, that could reasonably be considered to relate to the Senator’s position.”

The rule is followed by one exception: a gift can be accepted if it is “received as a normal expression of courtesy or protocol, or within the customary standards of hospitality that normally accompany the Senator’s position.”

Canada’s ethics commissioner, Mary Dawson, said Wednesday that she will investigate Wright’s cheque to Duffy.

But Liberal MP Ralph Goodale said authorities also need to be called in.

“The first thing is to make sure this is properly pursued by police,” he said.

The PMO said Wednesday that Wright will not be fired or asked to resign.

Duffy is one of three senators whose living expenses have come under public scrutiny following allegations that they were claiming tens of thousands of dollars annually for accommodations in the Ottawa area under the Senate’s housing allowance rule. The rule is intended to compensate those who live more than 100 kilometres from the capital, requiring them to maintain a secondary residence.

Evidence outlined in an independent audit last week showed that Duffy and two other senators -- Sen. Patrick Brazeau and Sen. Mac Harb -- spent more time in the capital than at the homes declared to be their primary residences, rendering their claims ineligible.

As a result of the audits, Brazeau was ordered to repay about $48,000 and Harb was ordered to repay $51,000.

While Harb and Brazeau have said that they will fight the Senate’s repayment orders, Duffy repaid the $90,172 in March.

After a Senate committee tabled reports on the secondary living expenses of the three senators last week, the government praised Duffy for showing “leadership” in paying back the funds. However, in the cases of Brazeau and Harb, the committee said the rules were “amply clear,” adding that the senators should not have claimed the allowance and must now pay it back.