The two nations have been locked in negotiations for a year on a rewrite of the 25-year-old continental trade deal that Mr Trump blames for losses of USA jobs and industry.
President Trump announced on Wednesday he rejected a meeting with the Canadian Prime Minister this week, as the countries struggle to strike a new North American trade agreement before a self-imposed October deadline.
US automakers and congressional aides now believe a deal with Canada is not possible by the deadline, which they said would most likely prompt the United States to move ahead with a bilateral agreement with Mexico.
Whether Congress will pass a deal that doesn't include Canada remains unclear. Last Thursday, she told reporters in Washington, D.C. that the atmosphere in the room "continues to be constructive".
Negotiations aimed at a new agreement have been underway for 13 months, but Canada and the US remain at loggerheads.
Lopez Obrador's new government was eager to sidestep conflict with Trump and focus on domestic issues.
"The ball is up in the air and no one knows when it's going to come down", he said.
There are just days to go before the latest USA -imposed deadline.
Trudeau's interactions with the mercurial USA president have been a subject of great curiosity over the course of his three days at the General Assembly.
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He was asked if he had denied Trudeau a request for face time while the two leaders were at the UN.
It wasn't immediately clear whether Trump was responding to comments Trudeau made earlier at a news conference of his own - similar to what happened over the summer following the G7 meetings in Quebec. "It's to defend Canada's interests, stand up for Canadians".
Canadian Prime Minister Justin Trudeau shrugged off USA pressure to quickly agree to a deal on the North American Free Trade Agreement (NAFTA) and indicated it was possible the three member nations might fail to conclude a new pact. The White House did not comment in response to Reuters questions.
The three countries are negotiating a new NAFTA deal. Canada used the process to defend its lumber exports in the face of US charges that the timber is unfairly subsidized.
Disputes have also arisen between over President Trump's request for increased access to Canada's protected dairy market.
At a separate event in New York, Canadian Prime Minister Justin Trudeau addressed trade tensions alongside his foreign minister, Chrystia Freeland, who is leading Nafta talks.
Pena Nieto needed an agreement by the end of August. US crude oil futures settled almost 1 per cent lower at $71.57 a barrel. "I think it's important to keep North America together, even if it takes more time" he said.
Personal connections also smoothed the path to a deal.
Trump cast serious doubts on the negotiations. The two men had met through Wall Street connections before Trump's inauguration in 2017. He also said dairy is a sticking point. He said that's why the US had an average eight hundred billion dollars a year in trade losses over five or six years.