His political rivals had earlier pounced on the news to criticize Harper's handling of Canada's response to the Syrian refugee crisis.
The Globe and Mail reported that the prime minister's office had directed immigration officials to temporarily halt processing Syrian refugee claims several months ago, effectively delaying their resettlement in Canada.
The claims were to be vetted and approved personally by Harper, the newspaper said, meaning fewer cases were ready for sponsorship when Canadians came forward in large numbers following the drowning of three-year-old Aylan Kurdi in August.
Harper said his office had asked for a security "audit" of the process.
His Tory government, he added, has taken a "generous approach to the admission of refugees while ensuring the selection of the most vulnerable people and keeping our country safe and secure."
"Political staff are never involved in approving refugee applications. Such decisions are made by officials in the department of citizenship and immigration," he said.
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Liberal leader Justin Trudeau earlier called the government's actions "irresponsible," saying it was an unacceptable "interference with important processes where lives are at stake."
Thomas Mulcair, leader of the New Democrats, said that the affair showed "abject behavior by Stephen Harper."
"It is a shame on Canada."
Canada's election is scheduled for October 19.
Harper faced strong criticism earlier in the campaign for not doing more for migrants, as a crisis unfolded in Europe with a record influx of people fleeing war in Syria.
The Tories last month committed to accepting 10,000 refugees within one year by simplifying and speeding up the application process, while stressing the key to ending the crisis was to defeat the Islamic State group.
The Liberals called for resettlement of 25,000 refugees by year's end and the New Democrats pledged to take in 46,000 over four years.