China's move had "seriously impacted regional safety and stability", the ministry said in a statement.
There was no immediate reaction from Beijing, which views Taiwan as a renegade Chinese province.
Huang Chung-yen, a spokesman for Taiwan's Presidential Office, said Beijing "should stop behaviour of this sort, which endangers regional peace, and not be an international troublemaker".
President Tsai Ing-wen had urged the army "to complete all tasks on war preparation", he added.
China has repeatedly sent military aircraft and ships to circle Taiwan during drills in recent years and worked to isolate the island internationally, whittling down its few remaining diplomatic allies.
The United States last week sent Navy and Coast Guard ships through the Taiwan Strait, as part of an increase in the frequency of movement through the strategic waterway despite opposition from China.
Taiwan is one of a growing number of flashpoints in the US-China relationship, which also include a trade war and China's increasingly muscular military posture in the South China Sea.
China has never renounced the use of force to bring Taiwan under its control.
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