Secretary of Homeland Security Janet Napolitano says the United States will not treat the Canadian border differently from the Mexican border. (Joshua Roberts/Reuters)

A suggestion by the U.S. Homeland Security Secretary that terrorists have routinely entered the United States through Canada — including the perpetrators of the Sept. 11, 2001, attacks — caused a kerfuffle in Washington Tuesday.

Janet Napolitano made the comment in an interview Monday with CBC's Washington correspondent, Neil Macdonald.

In the interview, Macdonald asked Napolitano to clarify comments she made last month that the Canadian and Mexican borders must be treated equally.

"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," Napolitano 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 Macdonald asked if she was referring to the 9/11 perpetrators, Napolitano answered: "Not just those but others as well."

Wilson 'frustrated' by comments

That prompted Michael Wilson, Canada's ambassador to the United States, to set the record straight Tuesday.

Wilson told reporters at the Border Trade Alliance meeting in Washington, where he was keynote speaker, that he is "frustrated" that the 9/11 myth has surfaced yet again.

"Unfortunately, misconceptions arise on something as fundamental as where the 9/11 terrorists came from," he said.

"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."

Napolitano misunderstood question, handlers say

In response to Wilson, Napolitano's handlers said she had misunderstood Macdonald's question and was referring to Ahmed Ressam, the would-be bomber referred to as "the millennium bomber."

Ressam was arrested in December 1999 at Port Angeles, Wash., with homemade explosives in his rental car. He was later convicted of plotting to bomb the Los Angeles International Airport.

Napolitano issued a statement later Tuesday to clarify her remarks.

While she knows no 9/11 terrorists entered the U.S. through Canada, she said, "there are other instances … 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."

Wilson said he was satisfied with the clarification but still wants a face-to-face meeting with Napolitano.

Napolitano digs deeper hole

But then, Napolitano appeared to make matters worse by explaining to the border conference Tuesday why the Canada and Mexico borders should be treated equally.

"The fact of the matter is that Canada allows people into its country that we do not allow into ours," she said.

"That's why you have to have a border, and you have to have border policies that make sense."

Liberal MP John McKay, who was at the conference, said Napolitano's comments alarmed him.

"If you are, in fact, negotiating a managed border, and your negotiating partner believes a set of mythology, then you have problems," he said "You try to work on the basis of fact, not on the basis of myth."

Saying Canada is lax about whom it allows into the country is "plain nonsense," he added.

"I have a heavily immigrant riding, and I do visas all day every day, and one of the most difficult things I have to explain to my constituents is why is it that the United States granted a multiple-entry visa to the relatives but Canada won't," said McKay, who represents the Toronto-area Scarborough-Guildwood riding.

In the past, other high-profile U.S. politicians have also suggested a link between terrorists and the Canadian border, including Napolitano's predecessor, Michael Chertoff, who said last year that more than a dozen suspected extremists had been caught trying to enter the U.S. via Canada.

When she was senator, Hillary Clinton said tighter security was needed at the Canada-U.S. border because of 9/11.

With files from The Canadian Press