Wallin, a former journalist who now represents Saskatchewan in the Senate, has claimed about $321,000 in travel expenses since September 2010 that are the subject of an audit by an outside firm.
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"I have been involved in the external audit process since December 2012 and I have been co-operating fully and willingly with the auditors," Wallin said in a statement. "I have met with the auditors, answered all the questions and provided all requested documentation.
"I had anticipated that the audit process would be complete by now, but given that it continues, I have decided to recuse myself from the Conservative caucus and I will have no further comment until the audit process is complete," she said.
Marjory Lebreton, the government leader in the Senate, said Wallin has resigned from the caucus and will sit as an Independent senator.
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Prime Minister Stephen Harper has defended Wallin in the past over her travel claims.
"Her travel costs are comparable to any parliamentarian travelling from that particular area of the country over that period of time," Harper said in the House of Commons in February. "For instance, last year Senator Wallin spent almost half of her time in the province she represents in the Senate."
Wallin's departure from the Conservative caucus comes one day after Senator Mike Duffy's announcement that he was leaving the Conservative caucus "pending resolution" of questions about expenses.
Senator Mac Harb, whose expenses were also scrutinized by an outside auditor, quit the Liberal caucus after audit results were released and said he would dispute the findings.
A fourth senator whose expenses were subject to scrutiny, Patrick Brazeau, was removed from the Conservative caucus over a separate criminal complaint that is currently before the courts.
Deloitte's audit of Duffy, Harb and 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.
Earlier this week, it emerged that Nigel Wright, Harper's chief of staff, had written a personal cheque to cover the amount Duffy owed. The parliamentary ethics officer is examining whether Wright was in violation of the Conflict of Interest Act when he wrote the cheque for Duffy.
Wallin, Duffy and Brazeau were appointed to the Senate by Harper in December 2008.
Harper will be meeting with his caucus next Tuesday, one day earlier than usual, in order to accommodate official travel which will see him on a visit to Peru and Colombia from May 21 – 24.Suggest a correction