Spokesman Nicolas Doire says the department is aware they have been prevented from leaving the country, adding that Canadian consular officials in Malaysia are in contact with local authorities.
Foreign Affairs would not confirm the identity of the Canadians, citing privacy concerns, but Malaysia's foreign affairs ministry identified them as Lindsey Petersen and his sister Danielle Petersen.
A magnitude 5.9 earthquake on Friday sent rocks and boulders raining down the trekking routes on 4,095-metre-high Mount Kinabalu in eastern Sabah state on Borneo island.
Search efforts for six missing climbers continued on Sunday, after rescuers recovered 13 dead from a strong earthquake that had trapped scores of trekkers.
Sabah Deputy Chief Minister Joseph Pairin Kitingan blamed the tragedy on a group of 10 foreigners who "showed disrespect to the sacred mountain" by posing naked at the peak last week. He said a special ritual would be conducted later to "appease the mountain spirit."
Officials have said a group of foreigners — including two Canadians — broke away from their entourage and stripped naked before taking photos at the mountain peak on May 30.
Floyd Petersen said he was unaware of the allegations against his son and daughter but said they were travelling through Southeast Asia and had not mentioned the matter to him.
"Would you tell your parents you did this?" he said from his home in Wood Mountain, Sask. on Saturday, adding that the pair only called him periodically from their trip. "I don't have anything to say, I'm just absorbing this."
Local media reported Sunday that a senior official with the Sabah Parks said the Canadians could face charges in a native court for allegedly violating local native laws.
The Malaysian Insider reports that Datuk Seri Tengku Zainal Adlin told reporters at the Sabah Park headquarters in Kundasang on Sunday that the tourists were in police custody in Kota Kinabalu and could be charged as early as Monday.
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