The new machines, which work much like self check-in for airlines, allow passengers to feed in their citizenship documents and customs declarations without waiting in line to speak face-to-face with an agent.
Travel documents are still to be verified by border services before passengers are able to leave the customs area.
The Canada Border Services Agency describes the machines as "secure and innovative," and says they will help border agents do their job more effectively.
Pierre Provost, the agency's head of border services at Trudeau, says the addition of the 18 automated kiosks will reduce wait times and ensure passengers pass through as efficiently as possible
However the union representing those agents says it has concerns.
"We're cutting more and more contact with our agents," said union representative Jean-Pierre Fortin.
"For us, it becomes a question of security."
Budget cuts to border services mean adding more agents to cut down on passenger bottlenecks isn't an option.
Airport officials hope the machines, which are optional for passengers who don't want to wait in line to give their declarations to an agent, will help move things along during peak periods like afternoons in the busy summer travel season.
Provost said automating some of the more routine declarations could actually improve security by allowing agents to concentrate on cases that present potential risks.
The kiosks were first introduced as a pilot program in the Vancouver International Airport during the 2010 Olympics.
The 18 machines at Trudeau cost around $4 million.
The automated service will soon be expanded to many of the country's international airports.