But the Conservative senator's explanation — that confusing paperwork is to blame for his innocent mistake — isn't washing with opposition leaders in either of Parliament's two chambers.
Sen. James Cowan, Liberal leader in the upper chamber, says he doesn't understand how anyone could find the paperwork confusing.
What's more, Cowan questions whether senators who don't live, vote, pay taxes, hold health care cards and driver's licences in their so-called home provinces are even entitled to sit in the Senate at all.
By that standard, Duffy and possibly two other Conservative senators — Pamela Wallin and Dennis Patterson — may not meet the constitutional requirement that senators must reside in the provinces or territories they were appointed to represent.
NDP Leader Tom Mulcair is raising the same doubts in the House of Commons.
For its part, the government insists Duffy, Wallin and Patterson all maintain sufficiently deep ties to their home provinces or territories to meet the undefined constitutional residency requirement.
As for Duffy's housing allowance, the government is urging opposition parties to await the results of a committee investigation and an external audit.
Cowan's criticism is a marked departure from a rare display of bi-partisanship earlier this month, when he and Marjory LeBreton, the government's leader in the Senate, demanded a swift and public resolution to allegations that some senators have been abusing the housing allowance.
The allowance is meant to compensate those who maintain a secondary residence in the National Capital Region while performing their parliamentary duties. At least three senators — Duffy, fellow Conservative Patrick Brazeau and Liberal Mac Harb — are alleged to have claimed the allowance even though their primary residences are actually in the capital region.
Cowan and LeBreton jointly asked the Senate's internal economy committee to interview senators who have made questionable claims for the housing allowance to determine the validity of their claims and demand repayment, with interest, where necessary.
Those interviews began Monday.
Cowan said he didn't know how many senators are being interviewed or their names.
While he didn't name Duffy specifically, he made it clear he doesn't think his explanation for mistakenly claiming the allowance, when his primary residence is in Ottawa, holds water.
Cowan said he's filled out the same paperwork Duffy has called vague and confusing and found it clear and straightforward.
"In this declaration of primary and secondary residences, there's no confusion in my mind about this form," Cowan said in an interview.
Cowan noted that the declaration, which must be filled out yearly, first asks senators to tick a box indicating whether their primary residence is within 100 kilometres of Parliament Hill or further away.
Duffy would have had to tick the box indicating his primary residence is outside the capital region, even though he's owned a home in an Ottawa suburb since well before his appointment to the Senate as a representative of Prince Edward Island.
Only after that does the form ask senators to write in the address of their primary residence in the province they represent — the part which Duffy said confused him and led him to claim his P.E.I. cottage as his primary residence.
Cowan said if he'd found the declaration confusing, he would have sought advice.
LeBreton declined to comment on Duffy's explanation. But she noted that she and Cowan co-signed a letter to the internal economy committee asking that repayment be demanded from any senator found to have made invalid claims.
"While I cannot speak for Sen. Cowan, I personally would prefer to let the committee complete its work," she said in an email.
The committee has asked for an external auditor to examine the claims of Duffy, Brazeau and Harb. It has also asked all senators who claim the allowance to provide proof of residency, including copies of their health care card, driver's license and income tax return and a declaration as to where they vote in federal, provincial and municipal elections.
Those whose documentation left some doubt are now being interviewed.
As well, the committee has sought legal advice as to how residency — a concept not defined in the Constitution — should be determined.
Cowan said as far as he's concerned residency is straightforward: it's where a senator lives, pays income taxes, votes, receives health insurance and a driver's licence.
"I don't understand what the confusion is all about."
However, if Cowan's interpretation is correct, that could make Duffy, Wallin and Patterson ineligible to sit in the chamber. All three appear to reside primarily outside the province or territory they were appointed to represent.
Both Wallin, a Saskatchewan senator, and Duffy hold Ontario health care cards and appear to vote in that province as well.
The government, not surprisingly, takes a more flexible view of residency.
"Senator Patterson, Wallin and Duffy all own property in the provinces and territory they represent," Peter Van Loan, the government's House leader, told the Commons on Monday.
"They maintain deep, continuing ties to those regions. In fact, all three senators spend considerable time in their home provinces and territory."
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