The Canadian Broadcasting Corporation quoted "highly placed sources" as saying the suspects were under surveillance for more than a year.
The CBC reported that the investigation was "part of a cross-border operation involving Canadian law enforcement agencies, the FBI and the U.S. Department of Homeland Security."
Al Qaeda has long studied the possibility of attacks on railroad systems -- seeing them as cheap, relatively easy to carry out and with potentially devastating results.
The organization and its sympathizers have plotted attacks on railway systems in Spain and Germany. More than 200 people were killed and 1,700 injured in an attack that targeted several commuter trains in Madrid in March 2004.
In a document seized during the raid in Pakistan that left Osama bin Laden dead was evidence of an al Qaeda discussion to target rail lines in the United States, a law enforcement official told CNN in late 2011.
According to the document, al Qaeda members discussed as early as 2010 a plan to derail trains in the United States by placing obstructions on tracks over bridges and in valleys.
The plan, according to the document, was to be executed to coincide with the 10th anniversary of the September 11 attacks, though no specific rail system was identified, the official said.
News of the arrests Monday came the same day Canada's parliament debated an anti-terrorism bill.
Traditionally, al Qaeda's membership is seen as Sunni-dominated and not Shiite.
As a result, al Qaeda and Iran have not been viewed as allies.
"We have very little intelligence on al Qaeda in Iran," King said.
What is known is that bin Laden's son-in-law, Sulaiman Abu Ghaith, fled Afghanistan for Iran after the fall of the Taliban in 2001.
According to U.S. documents and officials, in addition to Abu Ghaith, other members of bin Laden's inner circle ended up in Iran, including the formidable military commander of al Qaeda, Saif al-Adel, and Saad bin Laden, one of the al Qaeda leader's older sons who has played some kind of leadership role in the group.
Saad bin Laden also helped one of his father's wives and several of his father's children to move from Pakistan to Iran, officials said.