The report comes just days after a Canadian government memo statedsenior economic adviser told Canadian officials that the Illinois senator's own comments about NAFTA were for "political positioning." The release of that memo helped Clinton defeat Obama decisively in Tuesday's Democratic primary in Ohio, where the trade treaty is unpopular.
On Wednesday, the Canadian Press quoted an unidentified source as saying that Ian Brodie, Harper's chief of staff, made the comment last week to a crew for Canada's CTV television network during a press gathering to discuss Canada's budget. According to a person with knowledge of the incident, the source was a CTV journalist.
The Canadian Press story said a CTV reporter asked Brodie about remarks by Clinton and Obama that they would seek to renegotiate NAFTA.
"He said someone from Clinton's campaign is telling the embassy to take it with a grain of salt. ... That someone called us and told us not to worry," the journalist quoted Brodie as saying, according to the report.
On Thursday, Clinton spokesman Phil Singer said the campaign "flatly denied" the suggestion that a Clinton adviser had told Canadian government officials to take the candidate's tough talk on NAFTA with "a grain of salt."
Brodie did not immediately respond to a call seeking comment.
"Ian Brodie is alleged to have made an offhand comment about a rumor to a reporter. He does not recall saying it," Sandra Buckler, a spokeswoman for Harper, said in an e-mail to The Associated Press.
Some Democrats, as well as Canadian opposition parties, have accused Harper's Conservative government of meddling in the U.S. primary elections - in which Obama is in a close race with Clinton for the Democratic Party's nomination.
In Ottawa, Canadian opposition parties demanded Brodie be fired.
Harper told lawmakers in Parliament that the government would investigate the entire affair, referring to the alleged leaks about both the Clinton and Obama campaigns.
"We're going to investigate this entire matter and take whatever action that is deemed necessary based on the facts that we are able to discover," Harper said, a day after he called the release of the memo unfair and possibly illegal.
Canada's New Democratic Party Leader Jack Layton blasted the alleged leaks.
"There can be no doubt about it: The leak from within the Canadian government has had an impact now on the American elections," Layton said. "That is about the worst thing a country could do to another country - to have an effect on their democratic process."
The U.S. ambassador to Canada called the release of the memo "unfortunate."
"The prime minister yesterday stated that it was regretful that it happened and it shouldn't have happened," Ambassador David Wilkins told the AP on Thursday. "Now we need to get it behind us and move forward and continue to actuate the positive and build on this great relationship we do have."
Both Obama and Clinton said last week they would use the threat of pulling out of NAFTA to persuade Canada and Mexico to negotiate more protections for workers and the environment in the agreement.
NAFTA is unpopular among many blue collar workers in the United States who say it has cost American jobs.
A CTV report last week by Washington-based journalist Tom Clark said that both the Obama and Clinton campaigns gave Canada assurances over NAFTA. But the report led with Obama, and all the attention since then has been on his campaign.
Clark told the AP he had multiple sources on his story including a senior official at the Canadian embassy in Washington.
His TV report said a senior member of the Obama campaign contacted Canada's ambassador in Washington and told him any tough talk on NAFTA would just be campaign rhetoric. The Canadian embassy and the Obama campaign have both denied this.
Clark's report also quoted sources as saying the Clinton campaign made "indirect contact" with the Canadian government to express their support for NAFTA. The Clinton campaign has denied this too.
A 1,300-word memo obtained by the AP on Sunday, widely circulated within the Canadian government, said Obama's senior economic adviser, Austan Goolsbee, told Canadian officials in Chicago that the debate over free trade in the Democratic presidential campaign was "political positioning."
Goolsbee later said his comments were misinterpreted, and Obama denied offering the Canadians any such ideas. "Nobody reached out to the Canadians to try to assure them of anything," Obama told reporters Monday in Texas.
Harper earlier denied his chief of staff leaked that memo, but didn't say anything about the CTV's report last week.
ABC last week reported that Brodie was Clark's source. Earlier this week, Buckler, the Harper spokeswoman, said "Brodie does not recall discussing the matter."
On Monday, Clinton seized upon the memo to criticize Obama.
"I think that's the kind of difference between talk and action that I've been talking about," Clinton told reporters while campaigning in Ohio. "It raises questions about Senator Obama coming to Ohio and giving speeches against NAFTA."
The Canadian Press report raises questions about the Clinton campaign doing the same.