The two had not previously been scheduled for bilateral talks ahead of APEC meetings in Honolulu which were to be followed by the North American leaders' summit on Sunday night.
But the death of Mexican Interior Minister Francisco Blake Mora in a helicopter crash on Friday has forced Mexican President Felipe Calderon to pull out of both the APEC and the so-called Three Amigos summit.
"Prime Minister Harper was profoundly saddened to learn of the death of Mexican Secretary of the Interior Francisco Blake Mora and other Mexican government officials in a tragic helicopter crash," said a statement from the prime minister's office.
"Prime Minister Harper regrets that he will not be able to pass along his condolences in person and will be speaking with President Calderon at the earliest possible opportunity."
Upon arriving in Hawaii late Friday night, a spokeswoman for the prime minister said no decision had been made about whether Harper and Obama would meet on their own instead.
A meeting could re-energize what otherwise may be a lacklustre few days for Canada in Hawaii.
While the 21 members of the Asia Pacific Asia-Pacific Economic Co-operation forum are expected to outline a series of steps to move forward with a trade agenda, the real meat of the meetings will be served on the sides at negotiations for the formation of a new economic bloc.
Doors to the Trans Pacific Partnership remain closed to Canada, and Japan's recent addition to the countries involved in the TPP is likely to have Canadian officials asking pointed questions over the next two days of APEC.
Membership in the TPP is coveted because the deal is being led by the U.S., and because it links together hotly-sought after markets in the Asian Pacific region.
Japan has announced no timetable for joining the group, only its intention to join, a senior Japanese government official said Friday.
But the inclusion of the world's third-largest economy would vastly expand the reach of the trade pact, which now includes the smaller economies of Chile, New Zealand, Brunei and Singapore. The U.S., Australia, Malaysia, Vietnam and Peru are negotiating to join.
Publicly, the Canadian government says it's not sure it wants to be part of the deal.
"Looking at Canada's interests, we'll have to consider whether membership in the TPP would align with our broader agenda of jobs and growth," said Sara MacIntyre, a spokeswoman for the prime minister's office, at a briefing in advance of the trip.
"We'll only pursue opportunities that are in the best interests of Canadian businesses and workers."
But behind the scenes, there is frustration that Japan — which protects its rice farmers in a way similar to how Canada's dairy farmers are protected — is at the table for TPP while Canadians aren't.
Canada's supply management policies are cited by observers as the reason the country hasn't been invited to TPP talks.
But it's up to Canada to change that, a recent study suggests.
"Part of the long-term payoff for the United States will be to extend the TPP to its larger trading partners, including Canada, but Canada’s continued preference for supply management programs remains a significant obstacle to our participation," wrote the University of Toronto's Wendy Dobson in a study commissioned by the Canada China Business Council and the Canadian Council of Chief Executives that was published last month.
"If we cannot or will not join TPP, then the fallback position could be the negotiation of a series of economic framework agreements with priority countries in Asia, or with some other regional Asian arrangement."
While Obama is leading TPP negotiations Saturday morning, Harper, Fast and Foreign Affairs Minister John Baird will be holding their own series of bilateral meetings with Asia Pacific leaders to keep the ball rolling on current deals.
Canada is negotiating foreign investment promotion and protection agreements with China, Indonesia, Mongolia and Vietnam.
While the Conservatives have stressed making access to Asia Pacific markets a priority, someobservers have suggested the government doesn't have a focused enough agenda.
"Canada needs a strategy that positions Asia at the centre of public policy efforts rather than as a nice activity for a few line departments," said a recent study by the Asia Pacific Foundation on what professionals and academics with interests in the region think of Canada's involvement to date.
The study says less than a third of Canadians even identify Canada as being part of the Asia Pacific region.
As of late Friday night in Hawaii, the prime minister's office wouldn't confirm who Harper will meet one-on-one, citing the potential for last minute changes.
But if he doesn't sit down with Obama either before or after APEC, it could be seen as a major snub.
The U.S. president has meetings scheduled with the prime minister of Japan and the presidents of China and Russia.
The Harper government has been angling for an opportunity to meet with Obama to promote the border security agreement.
A face-to-face would also allow Harper the opportunity to raise the Keystone project directly with the president.
The proposed TransCanada pipeline faced a major setback this week with a U.S. decision to reroute the line and have it undergo more environmental assessments.