Taiwan criticized China's move, citing an agreement in 2015 that Beijing would consult Taipei before commencing new flights in the region.
The airlines said they would give refunds to almost 25,000 passengers who'd already booked flights.
It has retaliated by blocking requests to operate 176 additional flights between Taiwan and China by two Chinese airlines during the Lunar New Year the most important holiday for both sides, when tens of thousands of Taiwanese working in China want to travel home.
Flights between Xiamen and Kinmen first started in 2000 in attempt to boost trade and exchange between China and Taiwan's outer islands.
The Civil Aviation Administration of China condemned authorities in Taiwan for refusing to approve 176 flights to be operated by China Eastern and Xiamen Air using the newly opened airway M503, saying the decision disregarded the welfare of people on both sides of the strait, according to a CAAC statement published January 19. The four routes were specifically designated for the strait of Taiwan which separates mainland China from the island.
Talks between China and Taiwan have stalled since Tsai Ing-wen, leader of the pro-independence Democratic Progressive Party, came to power in 2016.
"We never said that we wouldn't approve of the added flights by China Eastern or Xiamen Airlines". "All along we said we hope that the situation can meet the needs of travelers and that we can all discuss an appropriate arrangement for the added flights".
Kinmen and Matsu have both been under Taiwan's control since defeated Nationalist forces fled to Taiwan at the end of the Chinese civil war in 1949. The schedule for the flights was in addition to Taiwan's regular airline services which were created to deal with the high demand of air travel especially during the Lunar New Year holiday which is due to start on February. As a result, the Taiwanese government withheld approval of route applications from the Chinese airlines.
"Yesterday I met a relevant official from the International Civil Aviation Organization, and he said the M503 route has been assessed and approved of by them, it's safe and reliable", Wang said, referring to the main disputed route.