Hundreds of Palestinian-Canadians and their supporters demonstrated in front of Harper's Langevin Block office building before heading to the Israeli embassy a few blocks away.
As they marched past Parliament Hill, there were screams of "shame, shame" when a handful of pro-Israel demonstrators draped in an Israeli flag shouted "no more terror" from a nearby sidewalk.
Police and march organizers were able to contain the crowd and keep the two sides apart.
One after another, speakers condemned Harper's statements in support of Israel.
The prime minister has been steadfast in his insistence that Canada stands firmly at Israel's side in the ongoing conflict that has included rocket fire from Gaza into Israel and an Israeli ground and air offensive.
The fighting has resulted in the deaths of hundreds of people, mostly Palestinians, including women, children and Israeli soldiers.
Israel has maintained that it has a right to defend itself against what have been almost continuous rocket attacks from Hamas-controlled Gaza.
The Ottawa demonstration included members of an international group known as Jews United Against Zionism, which has called for the dismantling of Israel as a political state.
"For 66 years this illegitimate state has brought death and suffering to Arab and Jew alike," said Rabbi Yisroel Dovid Weiss of New York. "We must rally together and condemn this current attack against the Palestinian nation."
But Canada's Centre for Israel and Jewish Affairs says it is becoming increasingly concerned by recent anti-Israel protests such as those held in Calgary, the Toronto area and Montreal.
"We are alarmed that anti-Israel demonstrations in Canada have become an outlet for hateful vitriol, intimidation, and even violence against Jews," the centre's Shimon Koffler Fogel said in a statement.
"Such abhorrent incidents are not only an attack on the Jewish community, they are an attack on core Canadian values including respect for the law and for free speech."
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