That significant foreign policy difference has effectively aligned the Harper Conservatives with Obama's Republican opponents at a time when they are pushing the White House to approve the Keystone XL pipeline.
Canada has firmly backed Israel in refusing to ease sanctions, while the U.S., Britain, France, Germany, Russia and China have agreed to relax $7 billion worth of such measures for six months to help grease the negotiations.
Obama said in his speech Tuesday night that he would veto any congressional plan to impose new sanctions on Iran while the international effort is under way to curtail Tehran's nuclear program.
"If this Congress sends me a new sanctions bill now that threatens to derail these talks, I will veto it," Obama said.
"For the sake of our national security, we must give diplomacy a chance to succeed."
Obama's plea for some additional diplomatic space to help the negotiations was heard in Ottawa, but it has not swayed the Harper government from its unflinchingly hard stand towards Iran.
Canada continues to "appreciate the efforts" of U.S. Secretary of State John Kerry and the five other countries leading the talks with Tehran, but the government won't budge on sanctions, said Rick Roth, a spokesman for Foreign Affairs Minister John Baird.
"The deal cannot be abused or undermined by deception," Roth said in an email.
"The Iranian people deserve the freedom and prosperity that they have been denied for too long by the regime's nuclear ambitions. Until then, Canadian sanctions will remain tough, and in full force."
Canada's position is in lock-step with Israel, which views Iran as an existential threat.
Israel believes that Iran will use the easing of sanctions to buy time to mitigate their harsh economic effects, while continuing clandestine efforts to develop a nuclear bomb.
Harper offered his own public endorsement of Israel's position during his historic speech to the country's parliament last week — and he opened the door for deeper sanctions if the negotiations fail.
When asked if anything had changed after Obama's pointed warning about sanctions, Roth reprised Harper's exact language from his speech to say that nothing had.
"We truly hope that it is possible to walk the Iranian government back from taking the irreversible step of manufacturing nuclear weapons. But, for now, Canada's own sanctions will remain fully in place," Harper told Israeli lawmakers.
"And should our hopes not be realized, should the present agreement prove ephemeral, Canada will be a strong voice for renewed sanctions."
Obama's Republican opponents in Congress also oppose any relaxation of sanctions because they believe their strong negative impact on the Iranian economy is what spurred the Islamic regime to sit down and bargain.
But Harper's pro-Israel stand on Iran comes at a time when he is trying to persuade Obama to approve the Keystone pipeline, so Alberta oilsands bitumen can start flowing south of the border.
In the end, Obama likely won't link the Keystone decision to Canada's position on Iran, but it still is not helpful, said Roland Paris, the director of the Centre for International Policy Studies at the University of Ottawa.
"It's true that the Harper government has mismanaged its relationship with the U.S. and failed to build goodwill with the White House, and goodwill is exactly what Canada needs now as it presses for a positive decision on Keystone," Paris said.
"Being offside on Iran doesn't help."
Ben Rhodes, Obama's deputy national security adviser, said the interim sanctions relief is limited while the broader international sanctions remain in place, so countries should continue to enforce them.
"So we are still enforcing the rest of our sanctions. Other countries, like Canada, are still enforcing their sanctions," Rhodes told a White House briefing on Wednesday.
Rhodes said the U.S. clearly recognizes the "very firm line" Canada has taken on Iran, but also knows that it shares the goal of preventing Iran from developing a nuclear weapon.
"We believe that if we get a good agreement that places significant constraints on the Iranian program ... that we will share the details of that agreement with our allies, including Canada, and be confident that they could see the importance of resolving this issue diplomatically," he said.
On Iran, Canada now finds itself in a political camp with Israel and Saudi Arabia, separated from the U.S. and much of Europe, said Trita Parsi, president of the Washington-based National Iranian American Council.
"Even the French are on board. They may be more skeptical of some others, but they are on board," Parsi said.
He said the White House won't be overly offended by Canada's position, as long as it doesn't actively try to thwart the negotiations with Iran.
"If however there's an effort to influence the U.S. position, then that would be different," said Parsi.
"But I have not seen that; I have just seen the Canadians go their own way on this."
— With files from Alexander Panetta in Washington
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