Carignan replaces Sen. Marjory LeBreton, who has held the job since 2006.
The new leader, a lawyer and former mayor, was appointed to the upper chamber in 2009 and has been deputy leader since 2011.
The government leader's job once came with a seat at the cabinet table, but was downgraded in the summer cabinet shuffle.
Carignan comes to the job as the Senate struggles to deal with a scandal over expenses.
Harper says Carignan has the experience needed to increase transparency and accountability in the Senate.
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