The refusal to agree to the extra flights is being seen as retaliation from Taipei, after China opened up several new air routes - which both China Eastern and Xiamen Airlines have been using.
This has disrupted the plans for thousands of travelers ahead of a key period for travelling in the region; the Lunar New Year Holiday. China's launch of the new flights reportedly goes against a deal between Taiwan and China to first discuss certain flight paths before they come into operation.
Two Chinese airlines were forced to cancel hundreds of flights Tuesday, as tensions over air navigation between China and Taiwan rise.
They included a northbound route known as M503, which travels up the Taiwan Strait that divides China from the self-ruling island.
In an apparent counter-measure, the Taiwanese authorities have withheld applications for additional Lunar New Year flights from 2 Chinese airliners which are using the new routes.
Earlier in January, the Chinese government began operating new routes along the Taiwan Strait, which officials in Taiwan said were done without its consent.
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It said there was no danger to safety, and that the routes, which were aimed at easing congestion, would only be used for civil aviation.
China considers Taiwan a wayward province, and relations have cooled dramatically since Tsai Ing-wen of the independence-leaning Democratic Progressive Party took office as Taiwan's president in 2016.
Multiple daily flights connect the islands to mainland Taiwan, while Xiamen and Fuzhou are also busy airports.
The government slammed the move as reckless and politically motivated, adding it could threaten Taiwan's security and endanger flight safety.
The airline apologized to customers and said it was providing free refunds and rebooking for anyone booked on the now-cancelled flights.
However, Taiwan claimed that no consultations were made over the planned routes that the airlines meant to fly their planes and levelled unilateral action accusations towards the Chinese government.