Senior intelligence officials on both sides of the border refused to discuss the warnings, the security measures or the source of the threats other than to say they came from the Middle East.
Top brass in Canada's military say they were told about the warnings.
"Yes, we were made aware" of the threats, said Cmdr. Kevin Carle of the Canadian navy.
"And we would encourage bases and stations where American military personnel are serving to support the process."
Security officials in Washington confirmed publicly on Feb. 24 that Muslim militants had issued religious edicts blessing attacks on U.S. civilians and allied interests worldwide.
It's the first time such edicts, known as fatwas, have been issued against U.S. civilians, according to documents released by the Pentagon.
A memorandum from the Counter-terrorist Centre of the Central Intelligence Agency said the edicts call for "attacks on U.S. persons and interests worldwide and on those of U.S. allies."
It was distributed by a coalition of Islamic groups in London and by alleged guerrilla financier Usama Bin Ladin.
Both fatwas said attacks should continue until U.S. forces "retreat" from Saudi Arabia and Jerusalem.
While no one would confirm the edicts were the source of the concern in Canada, the first alert coincided with their issuance in early January.
"There was probably not a specific threat" against Americans in Canada, said Lt.-Col. Bill Darley, a Pentagon spokesman. "It was probably a general heightened awareness (by local commanders) because of tensions in the Gulf."
He referred questions to the U.S. State Department, where an official in the counter-terrorism section refused to comment.
The second alert came near the end of February as a showdown with Iraq over UN weapons inspection reached the boiling point.
The orders to "blend in" with Canadians were specific and extended beyond a relaxed dress code. Vehicle markings, such as bumper stickers and gate passes, that would identify owners as American were to be removed.
Families were told to keep young children within sight at all times and to reinforce the normal parental warnings about strangers.
"It scared the hell out of me," one American said in a telephone interview from an undisclosed Canadian base.
About 481 American military personnel and their families serve at naval and air bases across the country. U.S. intelligence officers described Canada as "the soft underbelly of North America" and warned their people not be lulled into a false sense of security by being in a friendly, peaceful country so close to home.
Terrorism experts say the image comes, in part, from embarrassing revelations in recent years that undesirables have gotten into Canada. A Somali warlord and suspect in a terrorist bombing of a U.S. barracks in Saudi Arabia made it past Canadian immigration checks.
The RCMP, which handles the safety of all foreign nationals in Canada, says the criticism is unfair.
"We all know the U.S.-Canadian border is the longest undefended border anywhere in the world," said RCMP spokesman Derek Johnson.
"We take great pride in that. But it also creates some unique challenges for law-enforcement agencies."
The RCMP is soft-peddling the crisis, said John Thompson, of the Toronto-based Mackenzie Institute.
"Canadians should be bloody-well concerned," he said.
"We've got every organized crime group (in the world here). We've got the political arm for a lot of insurgencies operating in Canada. It's a wide-open country and we have been begging for the world's problems."