Beijing views self-ruled Taiwan as part of its territory and claims jurisdiction over the body of water that separates the island from the Chinese mainland.
The Canadian vessel passed through the strait on Sunday and was the first to do so this year, Taiwan's foreign ministry said, coming days after two US ships made the passage.
Canada's actions "deliberately stir up trouble and undermine peace and stability across the Taiwan Strait", Li Xi, a spokesperson for the Eastern Theater Command of the Chinese People's Liberation Army (PLA), said in a statement.
The army had dispatched its naval and air forces to monitor and guard the passage of the ship, Li said, adding that the troops would "resolutely counter all threats and provocations".
Taiwan's defence ministry hit back on Monday, saying China was the "greatest threat to peace and stability in the Taiwan Strait".
The United States and its allies regularly pass through the 180-kilometre (112-mile) strait to reinforce its status as an international waterway, angering China.
A US destroyer and an ocean survey ship travelled through the strait starting on February 10, drawing criticism from China's military, which said it sent the "wrong signal and increased security risks".
Washington's latest passage through the strait was the first since US President Donald Trump took office in January.
Taiwan's defence ministry, meanwhile, said it recorded 41 Chinese aircraft and nine warships near the island in the 24 hours to 6:00 am on Monday.
Communist China has never ruled Taiwan, but it claims the democratic island as part of its territory and has threatened to bring it under its control by force.
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