The House of Commons has unanimously adopted a motion condemning the murder, and offering condolences to the family of Shabaz Bhatti.
Al Qaeda and the Pakistani Taliban Movement in Punjab province claimed responsibility for the killing, in leaflets left at the scene in Islamabad.
Harper notes that Bhatti's brother, Peter, is a Canadian citizen.
The motion also urges the Pakistani government to repeal the country's blasphemy laws.
The prime minister and the Commons motion also urged Pakistan to track down the killers and put them on trial.
"Canada stands against those who commit gutless acts of murderous violence and extremism, and calls for the Pakistani authorities to bring those responsible to justice," Harper said.
He said the blasphemy laws pose problems for religious minorities.
"Canada also continues to urge Pakistan to prevent the abuse of its blasphemy laws, which restrict freedom of religion and expression and have disproportionately targeted religious minorities, and to protect individuals who choose to speak out on these issues," he said.
The leaflets left at the murder scene denounced Bhatti as "an infidel Christian."
His slaying on Wednesday followed the January killing of Salman Taseer, a liberal Pakistani politician who was shot by one of his guards.
Both men had campaigned to change blasphemy laws that impose the death penalty for insulting Islam.