Applications for Nexus cards have increased about 17 per cent since Canada and the United States began to more aggressively push the program earlier this year, causing some delays in processing applications.
The Nexus cards are designed to make border security more efficient by allowing passengers who aren't considered a danger to go through customs more quickly, while border guards focus on travellers who have the potential to be high risk.
But some air carriers don't appear to be training their check-in staff to recognize the cards.
And one carrier, Air Canada, is insisting that passengers travelling to and from the United States carry a valid passport, regardless of whether they have "trusted traveller" status.
The company's website says: "When travelling with Air Canada, all passengers, including Canadian and U.S. citizens, are required to present a valid passport when travelling by air between Canada and the United States, even with a Nexus card."
U.S. carriers American Airlines, Delta and US Airways maintain policies on their websites stating that passports, and nothing else, will be accepted to get on board one of their planes.
Others, however, including Westjet and United Airlines, tell their passengers that either a passport or a Nexus card may be used.
All eight of Canada's major airports have designated lines at pre-boarding checkpoints where Nexus card holders can bypass long security lines. Card holders, however, still have to go through security screening.
Marc Weber Tobias, an investigative attorney and physical security specialist based in Sioux Falls, S.D., complained in a blog in early June that he had trouble using a Nexus card while flying with Delta Airlines.
Tobias experienced delays checking in while flying with Delta to Ottawa because the airline's front-line ticketing agents refused to recognize his Nexus card as valid identification.
"It would be really nice if the airlines would get their act together in order to facilitate the programs put in place by the U.S. and Canadian governments to expedite travel and make it easier on passengers that cross these borders," he wrote.
"Unfortunately, in my case, three seasoned employees did not have a clue as to what they were talking about."
Eventually, Tobias was able to board his flight after a Delta supervisor accepted his identification.
In May, the Canada Border Services Agency launched an enrolment blitz to increase the number of people applying for Nexus cards. That has resulted in some delays in processing applications, according to the U.S. Customs and Border Protection agency (CBP).
"Some airports have longer waits for appointments — 90 days or longer," CBP public affairs officer Stephanie Malin said in an email.
However, most Nexus enrolment centres "have wide appointment availability within the next 60 days," she added.
Governments on both sides of the border have been trying to increase enrolments and decrease the time it takes to get a Nexus card. It is supposed to take between four and six weeks for an application to be processed.
As of June 17, there were nearly 690,000 Nexus members, with roughly 4,500 new applications being received each week. But only about 162,000 of the total are Americans. The vast majority of card holders are Canadian citizens.
Applicants seeking to qualify for the Nexus program must show they have no criminal record or any violations of customs or immigration laws and pay a $50 application fee.
They are required to provide fingerprints, have the irises of their eyes scanned and submit to an interview with a United States Customs and Border Protection officer — although some people can now bypass the interview.