He has already endured a Senate expenses scandal that cost him his chief of staff and suffered another setback in his attempts to reform the upper chamber thanks to a recent Supreme Court decision.
Now, with 11 current vacancies and looming retirements, Harper is faced with 17 empty seats in the red chamber by the end of the year — not to mention the three former Conservative Senators who have been suspended for ineligible housing and living expenses.
And CBC News has learned Harper is under growing pressure from a number of Conservative senators to fill those empty seats.
The senators cite concerns about how the Senate, and committees in particular, will be able to operate. They also question whether the regions are being fairly represented given the vacancies.
By the end of July, Prince Edward Island will lose Senator Catherine Callbeck to retirement. With Mike Duffy's suspension, that means P.E.I. will be reduced to half of its active representation.
Premier Robert Ghiz says the island will be underrepresented in Ottawa and while he admits the Senate has not been operated as well as it could, he believes the prime minister could do something about that in the next round of appointments.
"This time, I would try to stay away from the partisan route or attack dogs," suggests Ghiz. "I think there are a lot of quality people out there who want to make a difference in our country, who want to contribute, and hopefully the PM will look at someone of that quality."
P.E.I. is not alone in losing out on regional representation. The province of Manitoba will also be down to half of its Senate seats in the coming weeks, with three out of six seats vacant. By contrast, Nova Scotia and New Brunswick each have only two seats vacant out of 10.
But while Conservative senators may be gently pushing him to name appointees, the prime minister has given no sign he intends to do so.
No constitutional requirement
Harper's stated preference is to send elected senators to the upper chamber. He has urged the provinces to hold elections for senate nominees, but only Alberta has proved willing to do so.
When the Supreme Court delivered its opinion that the federal government could not reform the Senate without the support of at least seven provinces, Harper said it meant Canada was "stuck in the status quo for the time being."
The Prime Minister's Office goes further, saying that as long as the Senate continues to be able to deal with government legislation there is no plan to fill any of those seats.
Hugh Segal, who recently resigned his seat from the Senate to head up Massey College at the University of Toronto, points out there is no constitutional requirement for the prime minister to fill the vacancies, nor does he think Harper should rush into it.
But the former senator does think Harper has an opportunity to make the Senate a different place — and to send a message.
"You and I could make a list of people from the sciences, from the arts, from business, from philanthropy, from community service, some of whom may have been involved politically — that's not a bad thing — some of whom may have had no partisan involvement ever in their lives, but who could be expected to be absolutely reasonable and thoughtful senators who would vote on matters based on their merits," Segal suggests.
Segal also says context is important.
"I think every prime minister has to look at the context in which he or she is operating, what is necessary — what's in the best interest of the country at the time."
Harper has named 59 senators since he became prime minister in 2006.
Also on HuffPost