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Nigel Wright, chief of staff for Prime Minister Stephen Harper, is shown appearing as a witness at the Standing Committee on Access to Information, Privacy and Ethics on Parliament Hill in Ottawa on Nov. 2, 2010.Sean Kilpatrick/The Canadian Press

Questions about the RCMP's independence in the politically sensitive investigation into the Prime Minister's Office are unfair, the force's commissioner says.

RCMP Commissioner Bob Paulson sent a letter this week to a New Democrat MP to defend the decision to drop the criminal probe into the actions of Prime Minister Stephen Harper's former chief of staff, Nigel Wright. Mr. Wright, who left the PMO last year, landed in hot water after he gave $90,000 to Senator Mike Duffy in the midst of an expense scandal in the Upper Chamber.

Commissioner Paulson said the RCMP followed a rigorous process before ending the probe earlier this month in consultation with prosecutors, stating the decision was made "without fear, favour or affection."

"This ongoing questioning of our operational independence is quite confounding for me, I have to tell you," he said in the letter to the NDP's Charlie Angus.

"The RCMP decided not to bring charges after we thoroughly and completely investigated the matter."

Stating that he wrote the letter himself, Commissioner Paulson chided "some quarters of the media" that have implied the force is too close to the government, stating the criticism was made "unfairly and unjustifiably, in my view."

Commissioner Paulson has mostly stayed out of the limelight since the minister of Public Safety publicly rebuked him in 2012 for speaking out about harassment in the RCMP.

However, he has emerged to defend the way his force probed Mr. Wright's dealings with Mr. Duffy, stating that the RCMP's reasons will eventually become public, likely in a court proceeding.

"Canadians should be informed of the work we have done here and the rationale behind concluding this particular aspect of our investigation," Commissioner Paulson said. "I can't tell you precisely when it will be except to say that it shouldn't be very long."

The Mounties were probing a secret $90,000 payment Mr. Wright made to Mr. Duffy. Mr. Wright quit as Mr. Harper's chief of staff in May, 2013, after it was revealed he had dipped into personal funds to reimburse taxpayers for questionable expenses claimed by the PEI senatorin an effort to make the controversy over them subside.

In November, 2013, the RCMP alleged in court documents that Mr. Wright committed bribery, fraud and breach of trust by bailing out Mr. Duffy.

The force announced on April 15 that it had dropped its investigation, stating that "the evidence gathered does not support criminal charges against Mr. Wright."

Mr. Angus wrote to Mr. Paulson on April 24 with questions about the way the case was handled.

"Like many Canadians, I do not understand how it can be that writing a secret personal payment out of the Prime Minister's Office to a sitting senator doesn't contravene the law," Mr. Angus wrote. "If Mr. Wright's actions did not cross this line, the average Canadian is justifiably left wondering where exactly the legal and ethical line is in Ottawa today."

After receiving the Commissioner's response, Mr. Angus told reporters he is happy with the promise that Canadians will eventually learn more about the RCMP's investigative process.

"No, we're not questioning the independence [of the RCMP]," he said.

The Mounties have referred the matter of the $90,000 payment to federal Conflict of Interest and Ethics Commissioner Mary Dawson for further review.

Speaking through his lawyer, Mr. Wright said he has been vindicated.

"My intention was to secure the repayment of taxpayer funds. I believed that my actions were always in the public interest and lawful," Mr. Wright said in a statement. "The outcome of the RCMP's detailed and thorough investigation has now upheld my position."

Sources have told The Globe and Mail the results of the investigation into Mr. Duffy will be made public in the near future.

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