The establishment of the new air route comes as China has been stepping up efforts to isolate Taiwan, which broke away when the Communist Party took control of China in 1949. Earlier this month, Chinese authorities forced big multinational corporations that do business in China, including the Marriott hotel chain and Delta Air Lines, to remove Taiwan from lists of countries on their websites.

China began raising the pressure on Taiwan after Ms. Tsai’s election in 2016. The government of President Xi Jinping of China cut off official communications channels, citing her unwillingness to subscribe to the notion that Taiwan belongs to “one China.” Mr. Xi, who has pledged to restore China to international greatness, has issued stern warnings to Taiwan, saying China will never relinquish control of any part of its territory, even though the Communist government has never ruled Taiwan.

In a New Year’s statement last month, Zhang Zhijun, minister of China’s Taiwan Affairs Office, put blame for the current tensions on the Tsai administration, accusing it of “indulging and conniving with ‘Taiwan independence’ forces pushing forward with ‘desinification’, ‘progressive Taiwan independence’ and all kinds of backwards policies.”

The failure to consult with Taiwan before establishing the air route is seen as a slap in the face aimed at Ms. Tsai. In 2015, when Taiwan was governed by the more China-friendly administration of Ms. Tsai’s predecessor, Ma Ying-jeou, Beijing and Taipei negotiated an agreement for China to use a similar air route over the Taiwan Strait for Chinese airliners flying the opposite direction, from north to south.

In a statement on Wednesday, China’s Taiwan Affairs Office said the route was an internal affair of China. It also said that the safe use of the earlier, 2015 route proved that there was no safety risk in flights in the Taiwan Strait.