Senator Mike Duffy has resigned from the Conservative caucus and will sit as an Independent amid controversy over his living and travel expense claims.

Duffy, a senator representing Prince Edward Island, said in mid-April that he had repaid more than $90,000 in housing and living expenses that had been inappropriately claimed over four years. The Senate committee on internal economy confirmed the $90,172.24 repayment.

This week, it emerged that Nigel Wright, the prime minister's chief of staff, wrote a personal cheque for $90,172.24 to repay Duffy's living expenses.

The parliamentary ethics officer is examining whether Wright was in violation of the Conflict of Interest Act when he wrote the cheque for Duffy.

"It is clear the public controversy surrounding me and the repayment of my Senate expenses has become a significant distraction to my caucus colleagues, and to the government," Duffy said in a statement issued Thursday evening.

"Given that my presence within the Conservative caucus only contributes to that distraction, I have decided to step outside of the caucus and sit as an independent Senator pending resolution of these questions."

Duffy described the situation as "difficult" saying that he and his family "are going to take some time away from the public."

Conservative sources told The Canadian Press the vast majority of Duffy's Senate colleagues had signed a petition calling for his ouster from caucus and were prepared to confront him with that petition at a meeting next Tuesday evening.

A Deloitte audit of three senators — Duffy, Mac Harb and Patrick Brazeau — looked at travel claims and the living allowance that senators can claim to stay in Ottawa if their primary residence is more than 100 kilometres away. Duffy, a former journalist, has a longtime home in Ottawa and a residence in Prince Edward Island. The living allowance is worth up to $22,000 a year. The audits were trying to determine whether the senators were properly claiming the allowance.

Before the audit was completed, Duffy said he would pay taxpayers back $90,172, but that he hadn't done anything wrong. He said the form senators use to declare their primary residence is confusing. The audit said the rules need clarification.

A Senate report recommended that Harb must repay $51,000 for housing and mileage claims dating from April 2011, and Brazeau must repay $48,000. As well, Harb's expense claims will be audited for a seven-year period before 2011. Harb subsequently quit the Liberal caucus and is contesting the report. Brazeau, who was already sitting as an Independent, having been kicked out of the Conservative caucus after he was charged in February with sexual assault, is calling for a public meeting on his case.

CBC News reported Thursday that Duffy is listed as being on Senate business for two days during the last federal election when documents show he was campaigning for the Conservatives in the Greater Toronto Area. The audit shows that Duffy was neither in Ottawa nor Prince Edward Island, but in an "other location" on Senate business on April 27 and 28, 2011.

The prime minister's office said Thursday the Conservative Party is reviewing Duffy's expense claims from the 2011 campaign.