The Taiwanese defence ministry's statement came a day after China's civil aviation authority said it was introducing changes to flights headed southwards along the M503 route starting from February 1.
The Chinese authority said the move was aimed at improving efficiency in a congested area.
However, Taiwan's defence ministry branded the adjustment as "unilateral and arbitrary".
The move, it warned, could "lead to an escalation in tensions", urging Beijing to "immediately" reverse the decision.
Transport Minister Wang Kwo-tsai also warned the route runs close to Taipei's flight information region -- just 4.2 nautical miles at its nearest point.
"When the weather is bad, (a plane) might fly east and this could clash with our civil and military aircraft," he told reporters.
Route M503 had sparked an outcry in Taiwan when China launched it in 2015, given its proximity to the median line that runs through the Taiwan Strait.
China, which claims self-ruled Taiwan as part of its territory and does not recognise the median line, on Wednesday reiterated its position.
"Route M503 is a civil route," China's Taiwan Affairs Office spokesperson Chen Binhua said, adding that there is no "so-called median line".
"This route was launched to alleviate congestion in the relevant airspace and ensure aviation safety," he added.
The announcement follows the election in Taiwan of the independence-leaning Lai Ching-te, whom Beijing had branded a "severe danger".
Beijing has vowed to seize Taiwan, by force if necessary, and ramped up pressure on the island, staging several rounds of major military drills in the Taiwan Strait in recent years.
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