Harper offered his government's most conciliatory view to the visa that it imposed in 2009 to stop an influx of bogus refugee claimants. It came after his Parliament Hill meeting with Mexico's president-elect Enrique Pena Nieto.
Mexico was stung by the visa requirement, viewing it as heavy-handed and unexpected.
"We would ultimately like to see visa-free travel with Mexico," Harper said at a joint news conference, standing next to the new, young telegenic Mexican leader, who will be sworn in Saturday as president.
But first, the government is working to change its immigration system first so there is not a recurrence of past problems, Harper added.
"We have changed laws. We're in the process of changing our systems," said Harper.
It would be in the interest of both countries to get rid of the visa, he added.
Pena Nieto acknowledged the Canadian rationale for imposing the visa, breaking with the harder line against it taken by his predecessor Felipe Calderon, who is completing the single six-year term that Mexico's constitution allows.
"As Mr. Harper said, this is the result of excessive refugee claims that were perhaps unfounded — citizens of our country who claimed refugee status, which got them access to social security benefits in this country."
Pena Nieto said he asked about the Canadian legislative changes during his meeting with Harper. "I do hope that once the legislation is approved in the near future we will be able to avoid this requirement."
The Canadian Chamber of Commerce and the Centre for International Governance Innovation argued in favour of the visa's removal in a joint paper prior to Pena Nieto's arrival.
Pena Nieto was making the one-day whirlwind visit to Ottawa after travelling to Washington to meet with President Barack Obama, just three days before being sworn in as Mexico's new president.
Obama praised Pena Nieto's ambitious reform agenda and expressed confidence the two countries would strengthen economic and trade ties and increase security along their border.
Pena Nieto was in Canada to reach out to Mexico's other North American trade partner.
Prior to his arrival, the incoming Mexican leader said he wants to encourage Canadian investment in his country's state-run oil company.
But he made clear Thursday that his country has no intention of privatizing the company, Petroleos Mexicanos.
In its joint paper, the chamber and CIGI noted Canada's energy sector has new opportunities in Mexico as Pena Nieto takes power.
"With President-elect Pena Nieto's promise to allow foreign investment in the Mexican petroleum sector, there is, for example, a window of opportunity for Canadian energy firms to look for opportunities in Mexico."
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