The Civil Aviation Administration of China (CAAC) announced that it is opening four routes to help ease congestion in its airspace over the Taiwan Strait, which separates the island from mainland China.
But Taipei said Beijing had not consulted it over the move which "ignores flight safety and disrespects Taiwan."
"We believe... this is purposefully using civil aviation as a cover for improper intentions regarding Taiwan politics and even military affairs," Taiwan's Mainland Affairs Council said in a statement.
China's first attempt to open it in 2015 sparked protests that prompted Beijing to move it closer to the mainland and use it only for north-to-south flights.
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"The rapid growth of flights in western Taiwan Strait airspace in recent years has caused increasingly serious delays," CAAC said today.
The M503 can now be used for south-to-north flights too, it announced, adding the four new routes are only for civilian flights and that China will maintain technical communications with Taiwan.
China and Taiwan split after a civil war in 1949 and the island has been self-ruled since. But Beijing still claims it as part of its territory to be brought back into its fold -- by force if necessary.
Beijing has also exerted military pressure on Taiwan's airspace by stepping up drills around the island.