Taiwan's air force sent up aircraft to intercept and warn the Chinese away, the ministry added.
Adding to the stepped up military action near Taiwan, the U.S. Navy said the guided missile destroyer USS John S. McCain conducted a "routine" transit of the Taiwan Strait on Wednesday.
China's Eastern Theatre Command said it tracked the ship and denounced the United States for "endangering the peace and stability of the Taiwan Strait".
Speaking earlier in the day, Taiwan Foreign Minister Joseph Wu said the United States was concerned about the risk of conflict.
"From my limited understanding of American decision makers watching developments in this region, they clearly see the danger of the possibility of China launching an attack against Taiwan," he told reporters at his ministry.
"We are willing to defend ourselves without any questions and we will fight the war if we need to fight the war. And if we need to defend ourselves to the very last day we will defend ourselves to the very last day."
China's Taiwan Affairs Office and the U.S. State Department did not respond to requests for comment on Wu's remarks. China has said its activities around Taiwan are aimed at protecting China's sovereignty. The United States has expressed concern about China's movements, and said its commitment to Taiwan is "rock solid".
Neither Taiwan nor China has said precisely where the Chinese carrier group is, or whether it is heading towards the disputed South China Sea, where a U.S. carrier group is currently operating.
Speaking in parliament, Taiwan's Deputy Defence Minister Chang Che-ping said the Chinese carrier's movements were being closely followed, and described its drills as routine.
A person familiar with Taiwan's security planning told Reuters the carrier group is still "near the Japanese islands", declining to disclose the exact location. Japan had said on Sunday that the Chinese carrier group had entered the Pacific after sailing through the Miyako Strait, through Japan's southern Ryukyu island chain northeast of Taiwan.
Washington, Taiwan's most important international backer and arms supplier, has been pushing Taipei to modernise its military so it can become a "porcupine", hard for China to attack.
Wu said Taiwan was determined to improve its military capabilities and spend more on defence.
"The defence of Taiwan is our responsibility. We will try every way we can to improve our defence capability."
Taiwan's Defence Ministry said it will run eight days of computer-aided war games this month, simulating a Chinese attack. A second phase of exercises, including live-fire drills and anti-landing drills, will take place in July, when hospitals would also practice handling mass casualties.
"The drills are designed based on the toughest enemy threats, simulating all possible scenarios on an enemy invasion on Taiwan," Major General Liu Yu-Ping told reporters.
Asked if Washington's de facto embassy, the American Institute in Taiwan, would send representatives to the drills, Liu said such a plan was "discussed" but "will not be implemented", citing military sensitivity.
(Reporting By Ben Blanchard and Yimou Lee; Additional reporting by Roger Tung; Editing by Simon Cameron-Moore and Peter Graff) ((firstname.lastname@example.org; +886-2-8729-5122;))