China claims self-ruled Taiwan as part of its territory and has stepped up military and political pressure as relations have plunged in recent years.
The navies of the United States and its Western allies, meanwhile, have increased "freedom of navigation" crossings through the strait to reinforce its status as an international waterway, angering Beijing.
Taipei said Thursday that the Canadian ship's transit took place Wednesday, with the warship travelling "from north to south".
"The military has monitored the situation and no anomaly was detected in our surroundings," the defence ministry statement said.
Li Xi, a spokesman for the Chinese military's Eastern Theater Command, condemned the passage.
"Canada's actions disturbed the situation and undermined peace and stability in the Taiwan Strait," Li said.
"(Our) troops are always on high alert and ready to respond to any threats and provocations at any time," he added.
The Halifax-class frigate "HMCS Montreal recently conducted a routine transit through the Taiwan Strait", the Canadian Joint Operations Command confirmed on social media platform X without providing a date.
"Canada supports the rules-based international order by operating in accordance with international law," it said.
"Our activities promote peace, resilience, and security in the Indo Pacific."
Though Taiwan has only a dozen diplomatic allies, it maintains strong partnerships with various Western democracies like the United States, which is its biggest weapons seller.
Last November, US and Canadian warships passed through the Taiwan Strait, their second joint passage in two months -- a move that put Beijing's armed forces on "high alert", according to China's Eastern Theater Command.
Taiwan's military has been reporting near-daily sightings of Chinese warships around its waters, as well as sorties by drones and fighter jets around the island.
On Thursday, the defence ministry said 29 Chinese military aircraft and 10 naval vessels were detected in a 24-hour window ending at 6:00 am (2200 GMT Wednesday).
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