A statement posted on Harper's website says Canada is worried about reports of political leaders and journalists being intimidated and jailed and the harassment of minorities along with alleged disappearances and killings.
Harper was attending the 21-member Asia-Pacific Economic Cooperation summit that ended today on Indonesia's resort island of Bali.
"Canada is deeply concerned about the situation in Sri Lanka," the statement said. "The absence of accountability for the serious violations of human rights and international humanitarian standards during and after the civil war is unacceptable."
There are 54 Commonwealth members, a loose association of former British colonies.
Sri Lanka's three decades of civil war ended in May 2009 with the defeat of the Tamil Tiger rebels who were fighting for a homeland for the Tamil minority.