The RCMP have laid 31 charges against suspended senator Mike Duffy, including fraud and breach of trust, wrapping up a criminal investigation that stretches back more than a year and reigniting the Senate expenses scandal.

The investigation began with a probe of housing expense claims for a home where Mr. Duffy resides in Ottawa, but expanded to include expense claims for personal or party-related travel, the awarding of consultant contracts where funds were allegedly used for personal gain and the circumstances under which the senator asked for, and received, a $90,000 cheque from former Harper chief of staff Nigel Wright.

The charges include seven counts of fraud over $5,000, seven counts of fraud under $5,000, 15 counts of breach of trust and one count each of bribery of a judicial officer and frauds on the government. (Read the full list of charges)

Story continues below advertisement

Mr. Duffy will appear in an Ottawa court on Sept. 16 on the charges.

Commanding Officer Gilles Michaud of the RCMP's National Division said investigators sifted through four years' worth of expense claims, bank statements, phone records and thousands of emails.

Speaking through his lawyer, Donald Bayne, on Wednesday night, Mr. Duffy maintained his innocence and said he looks forward to a fair hearing in court where he will mount a vigorous defence.

"Senator Duffy is thankful that the awful 16 months of waiting through a protracted and highly public police investigation is finally over and we can move on to an impartial forum and fair hearing," his lawyer said, reading a statement.

"To date, Senator Duffy has never had a fair hearing either in the Senate or in the media. We're confident that when the full story is told, as it will be, and shown to be supported by many forms of evidence, it will be clear that Senator Duffy is innocent of any criminal wrongdoing."

The Prime Minister's Office described Mr. Duffy's alleged conduct as "disgraceful" and said rule breakers must be punished but declined to make further comment.

"We have assisted the RCMP throughout their investigation, and congratulate them on the progress they have made," director of communications Jason MacDonald said in a statement.

Story continues below advertisement

"Those who break the rules must suffer the consequences. The conduct described in the numerous charges against Mr. Duffy is disgraceful. As this is now a criminal matter that is before the courts, we have nothing further to add."

The probe of Mr. Duffy largely centred on his living allowances, with the RCMP investigating housing-cost claims the PEI senator submitted for what he designated as his secondary, or part-time, residence in the Ottawa area.

It also looked at the secret $90,000 payment that Mr. Wright, Stephen Harper's former chief of staff, made to Mr. Duffy – an effort to make the public controversy over the improper housing claims subside by providing funds necessary for the senator to return expense payouts he'd charged to taxpayers.

This past April, the RCMP dropped its criminal investigation into Mr. Wright, lifting the biggest cloud hanging over the Prime Minister's Office in the ongoing Senate scandal. The wealthy businessman 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 Mr. Duffy's questionable expenses.

With Mr. Duffy now facing charges, the governing Conservatives, who have been dogged by the Senate expenses controversy for nearly a year, face a further public airing of the PMO's efforts to manage fallout from the matter.

"I am sure that I am not the only Canadian who will now wonder openly how what was not a crime or a bribe when Nigel Wright paid it on his own initiative became however, mysteriously, a crime or bribe when received by Senator Duffy. The evidence will show that Sen. Duffy did not want to participate in Nigel Wright's and the PMO's repayment scenario, which they concocted for purely political purposes," Mr. Bayne said.

Story continues below advertisement

His lawyer said a trial will show his client was not to blame.

"There is much that is offensive here. But the evidence will show that it did not emanate from Sen. Duffy."

The RCMP have expressed their interest in seeing Mr. Wright testify if the matter goes to court, The Globe reported in April.

A separate investigation by the Mounties into Senator Pamela Wallin, also appointed to the Red Chamber by Mr. Harper, is still not complete, with much work left to examine her agendas and probe her expense claims.

Mr. Duffy's lawyer called on critics to dial back their pronouncements of Mr. Duffy.

"Those, including many in the media, who have been so eager and quick over the past year and a half to malign, and even libel Senator Duffy without his ever having had a fair hearing, should slow down their rush to judgment and let fair process determine this matter," Mr. Bayne said.

Story continues below advertisement

The biggest problem Mr. Duffy has faced is scrutiny of his housing claims.

Senators can charge taxpayers for tens of thousands of dollars of housing and meal expenses annually if their primary residence is located more than 100 kilometres away from Ottawa and they need to maintain a secondary residence in the capital region.

There is evidence, however, that Mr. Duffy spent more of his time in Ottawa, where he'd previously lived and worked for decades as a journalist, rather than at his Prince Edward Island residence and the RCMP have been probing the $90,000 in expenses he filed for his Ottawa-area home.

In addition, the RCMP had been looking into $64,916.50 in contracts that went to Gerald Donohue, one of Mr. Duffy's friends. According to documents filed in court by the RCMP, Mr. Donohue "acknowledged that he produced no tangible work product for Duffy" and instead provided online research and verbal advice on subjects "such as obesity, or being a Conservative."

The RCMP has already charged former Liberal senator Mac Harb and Harper appointee Patrick Brazeau over their Senate expense claims, ensuring the controversy will continue for months, and likely years. Mr. Harb has since resigned from the Senate.

Mr. Bayne said 2014 has been a hard year for Mr. Duffy and his wife.

Story continues below advertisement

"This has been a difficult year for Mike and Heather Duffy financially, emotionally and, for Mike, health wise. He's had to undergo a second open-heart surgery, required follow-up serious invasive medical procedures at the University of Ottawa Heart Institute and still has serious ongoing heart problems," the statement said.

"Despite Senator Duffy's serious, ongoing health problems which compromise his strength, and despite his limited resources, he intends to defend fully and fairly and to show that the truth and innocence are on his side," Mr. Bayne continued.

Both Mr. Duffy and Ms. Wallin are former broadcasters who were tapped for the Senate as Conservatives in December 2008 by Mr. Harper. They have since both been ejected from the party's caucus and are currently suspended from the Red Chamber.