The source, who spoke on condition of anonymity, was responding to a CBC News report that Duffy was worried he wasn't eligible to take a Prince Edward Island seat in the Upper Chamber.
CBC News reported Tuesday that Duffy asked to be named from Ontario rather than P.E.I. but Harper told him he needed to fill an Island seat.
A spokesman for the Prime Minister's Office on Tuesday refused to comment because the case is before the Ontario Superior Court. Duffy has pleaded not guilty to 31 charges of fraud, breach of trust and bribery.
Duffy moved to Ottawa in the 1970s to report from Parliament Hill. He bought his current suburban Ottawa house five years before Harper named him to the Senate.
On his way into court again today, Duffy wouldn't say anything when asked directly about his eligibility and what he told Harper.
'Protecting Stephen Harper'
For Tom Mulcair, leader of the Official Opposition NDP, it could explain why Stephen Harper's office seemed so concerned with Duffy. Mulcair pointed to the months of questions Harper endured in the House of Commons, the more than $90,000 his chief of staff gave Duffy to pay his Senate expenses, and the ever-shifting explanations for what happened.
"The Constitution said they have to reside in that province. So everyone's been asking the same question since the beginning," Mulcair said.
"And the answer is starting to be clearer and clearer: Stephen Harper was protecting Stephen Harper."
CBC News has pieced together the evidence from Duffy's criminal trial, which shows Duffy clearly scrambling to deal with questions of residency.
On Dec. 22, 2008, Duffy was named to the Senate with 17 others.
He met with Senate officials the very next day, but did not sign his residency declaration.
On Dec. 29, 2008, he went back to Prince Edward Island on his first official trip. Three days later, both he and his wife got their P.E.I. driver's licences.
Finally, Duffy signed his primary residence declaration on Jan. 6, 2009, which allowed him to tap into the $20,000-a-year Senate living expense budget.
'Out of touch'
It's that budget the RCMP alleges was used fraudulently for personal and partisan reasons.
Although the number of questions about Duffy had diminished recently in question period, that was not the case today.
"Even Mike Duffy himself was so concerned about not meeting the constitutional residency requirements to be a senator from Prince Edward Island that he asked the prime minister to appoint him from Ontario," Liberal MP Dominic Leblanc said.
"Is the prime minister so out of touch he thought he could bypass the Constitution, appoint Mike Duffy from Prince Edward Island, just for the chance to get up and feign indignation that he recently discovered that Mike Duffy has lived in Ottawa for 40 years?"
Paul Calandra, Harper's parliamentary secretary, said the Conservatives have been fighting to bring accountability to the Senate while the NDP and Liberals "were trying to make victims out of these people."
"The constitutional practice on this [has] been clear for almost 150 years, Mr. Speaker," Calandra said.