Harper has threatened to ignore the 54-country summit that Sri Lanka hosts later this year because he has serious concerns about Colombo's commitment to human rights and democracy since the country's long civil war ended in 2009.
The latest flashpoint came Friday after President Mahinda Rajapaksa dismissed the country's chief justice, Shirani Bandaranayake, after a widely condemned impeachment process.
The move sparked protests Monday in the South Asian country and raised fears of a constitutional crisis if the government moves to replace Bandaranayake.
"We call on the government of Sri Lanka to respect the country's constitution and the independence of its judiciary and change course immediately," Harper said in a statement.
Harper said he is deeply concerned by the move, which he said came after "an impeachment process which appeared to be highly politicized and lacking transparency and respect for the guarantees of due process and fair trial."
NDP foreign affairs critic Paul Dewar called on Harper to "state unequivocally" that he will boycott the Commonwealth summit in Colombo.
"We urge Commonwealth members to step up action to condemn this attack on judicial independence," said Dewar.
Harper said Canada will push for the matter to discussed at the next meeting of the Commonwealth's ministerial action group, set for April.
Gordon Campbell, Canada's high commissioner to the United Kingdom, spoke with the secretary general of the Commonwealth last week and requested that Sri Lanka be added to the group's next meeting, said Rick Roth, spokesman for Foreign Affairs Minister John Baird.
Canadian officials also expressed their concerns directly to Sri Lanka's high commissioner to Canada in a meeting on Friday, and will be talking to Sri Lankan government officials in Colombo as well, Roth said.
"Canada continues to have serious concerns about the human rights situation, the need for reconciliation, and the democratic deficit in Sri Lanka," Harper said.
"We will continue to raise these concerns forcefully, without equivocation both directly with the government of Sri Lanka and through resolutions at both the United Nations and the Commonwealth."
Interim Liberal leader Bob Rae called on Harper and Baird to press for an emergency meeting of the Commonwealth's ministerial action group.
"It is simply unacceptable that we wait to address this dire situation until the next scheduled meeting, as Prime Minister Harper and Minister Baird would prefer," said Rae, who was an adviser to the Sri Lankan peace process from 1999 to 2006.
Canada has been leading an international effort to press the Sri Lankan government to seriously examine allegations of summary executions, kidnappings and other atrocities by government forces and the Tamil Tiger rebels.
The violations are alleged to have occurred in May 2009 when government forces routed the Tigers to end the country's two-and-a-half decade civil war.
Canada co-sponsored a resolution at the UN Human Rights Council that pressed Sri Lanka to properly investigate the alleged war crimes.
An internal Sri Lankan commission into the matter has been widely criticized by Canada and others as a whitewash that favours the government.
A UN panel of experts has found that there are credible allegations of war crime and crimes against humanity.
"Canada has strongly supported resolutions at both the United Nations and the Commonwealth condemning the Sri Lankan government's lack of action on reconciliation and the country's disturbing slide in human rights," said Baird, who will represent Canada at the action group.
Commonwealth Secretary-General Kamalesh Sharma is to visit Sri Lanka next month.
"I will also consider further Commonwealth initiatives and responses as are envisaged in situations that could be perceived to constitute violations of core Commonwealth values and principles," he said after Friday's dismissal.
Since winning a second term as president following the end of the civil war in 2009, Rajapaksa has pushed through new laws that are seen as steps toward establishing absolute power.
He has extended term limits on the presidency and abolished independent commissions.
Bandaranayake's impeachment is seen as an attempt to muzzle the judiciary.
Recently, Bandaranayake ruled against Rajapaksa's brother, the head of Sri Lanka's economic development ministry.
The Rajapaksa family occupies many senior government positions, including head of the defence ministry and the speaker's chair in Parliament. One of Rajapaksa's sons sits as an MP.