The U.S. Homeland Security chief has clarified earlier remarks that suggested the 9-11 terrorists entered the U.S. through Canada.

Homeland Security Secretary Janet Napolitano made the comments during a media interview earlier this week, much to the chagrin of Canadians on both sides of the border.

In a release Tuesday night following the interview, she called Canada a "close ally and an important partner" and said she was simply misunderstood.

"I know that the September 11th hijackers did not come through Canada to the United States," she said in the statement.

"There are other instances, however, when suspected terrorists have attempted to enter our country from Canada to the United States. Some of these are well-known to the public -- such as the Millennium Bomber -- while others are not due to security reasons."

Ottawa rushed to defend its border security on Tuesday amid the diplomatic scuffle that broke out over Napolitano's earlier remarks.

In recent years, Ottawa has invested a great deal of effort into dispelling perceptions among Americans that Canada's border is an easy entry point for terrorists planning attacks on U.S. soil.

"Unfortunately, misconceptions arise on something as fundamental as where the 9-11 terrorists came from," said Michael Wilson, Canada's ambassador in Washington.

"As the 9-11 commission reported in 2004, all of the 9-11 terrorists arrived in the United States from outside North America. They flew to major U.S. airports. They entered the U.S. with documents issued by the United States government and no 9-11 terrorists came from Canada."

Wilson, who was the keynote speaker at the Border Trade Alliance meeting in Washington on Tuesday, said Napolitano's staff attempted to tamp down the controversy by blaming the comments on a simple misunderstanding.

"Her comment from her people is that she misunderstood," Wilson said, adding that he was planning a personal meeting with Napolitano in the near future.

The furor began when Napolitano was asked to clarify statements she had made about equal treatment for the Mexican and Canadian borders, despite the fact that a flood of illegal immigrants and a massive drug war are two serious issues on the southern border.

"Yes, Canada is not Mexico, it doesn't have a drug war going on, it didn't have 6,000 homicides that were drug-related last year," she said.

"Nonetheless, to the extent that terrorists have come into our country or suspected or known terrorists have entered our country across a border, it's been across the Canadian border. There are real issues there."

When asked if she was referring to the 9-11 terrorists, Napolitano added: "Not just those but others as well."

However, Public Safety Minister Peter Van Loan downplayed the comments and said that Napolitano is well aware that Canada was not the source of the 9-11 terrorists.

"We spoke about it back in March, and we were sharing a chuckle at the fact that the urban myth does circulate," he told CTV's Power Play.

"Ms. Napolitano understood quite clearly, then and now, that none of the September 11 terrorists came through Canada, as the 9-11 Commission found."

Still, that positive outlook wasn't shared by other Canadian officials.

On Tuesday afternoon, RCMP Commissioner William Elliot expressed frustration with the comments during an interview on CTV's Power Play.

"I was somewhat surprised and disappointed," he said, adding he hopes the misconception has been cleared up.

"I understand and am happy to hear that she has issued a statement acknowledging that that didn't happen."

But Thomas d'Aquino, president of the Canadian Council of Chief Executives, decried Napolitano's comments on Tuesday.

"I am a longstanding friend and ally of the United States, but sometimes failures in our two-way dialogue cause me to shake my head in sadness and dismay," he said in a press release.

"The claim that some of the 9/11 terrorists entered the United States from Canada is, quite simply, a myth - an urban legend that began with a handful of erroneous media reports in the days following the terrorist strikes."

With files from The Canadian Press