The People's Liberation Army's Eastern Theatre Command said the ships, the Canadian frigate Ville de Quebec and the Australian guided-missile destroyer Brisbane, were engaged in "trouble-making and provocation".
Chinese air and naval forces followed and warned the two ships and "effectively responded," the command said in a statement.
"The actions of the Canadians and Australians send the wrong signals and increase security risks," it said.
An Australian Defence Department spokesperson said on Sunday the Royal Australian Navy Hobart Class destroyer HMAS Brisbane conducted a routine transit through the Taiwan Strait from Saturday to Sunday "in accordance with international law".
"The transit was conducted along with Royal Canadian Navy frigate HMCS Ville de Quebec," the spokesperson said in a statement.
"Australian vessels and aircraft will continue to exercise freedom of navigation and uphold International Law, particularly United Nations Convention on the Law of the Sea."
A spokesperson for the Canadian armed forces said they do not comment on sail plans for currently deployed ships.
The spokesperson said the Ville de Quebec was deployed as part of Operation Horizon, meant to promote peace and stability in the Indo-Pacific region.
Ville de Quebec was operating in the Philippine economic zone earlier this week, participating in freedom of navigation exercises, according to a Canadian government statement.
China's state-backed newspaper the Global Times on Saturday reported on the mission.
Taiwan's defence ministry said in a statement it keeps a close watch on activity in the strait and "dispatches appropriate air and naval forces to ensure the security and stability" of the waterway, which separates Communist China from the democratic island of Taiwan.
The United States Navy and occasionally ships from allied countries such as Canada, the United Kingdom and France transit the Strait, which they consider an international waterway, about once a month.
Taiwan also considers it an international waterway.
China, which views Taiwan as its own, says the strategic waterway is part of its territorial waters.
Taiwan's government rejects territorial claims from officials in Beijing.
China has in the past five years increased its military pressure against the island, including staging war games near Taiwan.
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