Mulcair was responding to suggestions this week that Harper overrode Duffy's concerns about being appointed to the Senate to represent the province of Prince Edward Island in late 2008.
A source familiar with the details of those discussions told The Canadian Press that Duffy suggested he would be better placed as a senator from Ontario, since that's where he had lived for decades, but Harper was insistent about P.E.I.
That's when Duffy, who grew up on the island, began to make plans to renovate a cottage he owned there. He also designated his existing home in Ottawa as his secondary residence, triggering living expenses for that property.
Four years later, Duffy and the prime minister's office found themselves questioned about whether Duffy was in fact eligible to represent P.E.I.
The Constitution says senators must own $4,000 worth of property in the province they represent and that they must also be "resident" in that province.
The Prime Minister's Office did all they could in early 2013 to stave off questions related to the constitutional eligibility of Conservative senators.
"What we all had a bit of trouble understanding since the beginning of this whole Mike Duffy-Stephen Harper affair is, who was Stephen Harper protecting?" Mulcair told reporters Wednesday.
"... What we now realize is that Stephen Harper was protecting, of course, Stephen Harper."
Stephen Lecce, a spokesman for Harper, declined to comment on a matter before the courts.
A Conservative source said that it is not true that Duffy raised concerns about his qualifications before the appointment.
Harper has said that senators sign a declaration that they meet the constitutional requirements to represent the province and that is sufficient for determining eligibility.
"The constitutional practice on this has been clear for almost 150 years," Harper's parliamentary secretary Paul Calandra said during question period.
The actual declaration the senators sign only refers to the senator being "duly qualified to be a member of the Senate of Canada," and that the individual owns at least $4,000 worth of property in the province he or she represents. There is no specific reference to residency.
Duffy's trial on breach of trust, fraud and bribery charges has meanwhile been put on pause while lawyers argue over the admissibility of a Senate report.
Justice Charles Vaillancourt will hear arguments Monday in what is called a voir dire, basically a mini-trial within the main trial.
Donald Bayne, the suspended senator's lawyer, wants to treat a 2010 Senate committee report as fact during the course of the trial.
The report was based on an audit of senators' office expenditures and service contracts and is likely to be used by the defence to drive home the point that the Senate itself knew its rules were vague and confusing.
"The audits found that some administrative policies were outdated, inadequate, or non-existent," reads the report, prepared based on an audit by the firm Ernst and Young.
"They also found that, in certain instances, policies were poorly communicated and/or not well understood by users."
The Crown wants the report treated as opinion, not fact — an important distinction when the judge later reviews the evidence.
The unplanned break further delays the trial, which is already expected to overrun its 41-day schedule by weeks.
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