The island's Civil Aeronautics Administration (CAA) said the opening of the routes, originally set for Thursday, would now be delayed pending further negotiations.
"The two sides agreed that the... Flight routes will be postponed," the CAA said in a statement, with more discussions planned.
"We feel negotiations have been positive and we support the solution of problems through mutual trust and rational negotiations, as well as efforts to safeguard peace and development across the Taiwan Strait," it said.
However Taiwan slammed the unilateral move as "unacceptable" and said it posed a potential air defence threat.
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The routes would take planes over the Taiwan Strait from China's coastal province of Zhejiang and the cities of Fuzhou and Xiamen in Fujian province.
Cross-strait ties have improved markedly since Ma Ying-jeou from the China-friendly Kuomintang party came to power in Taipei in 2008. He was re-elected in 2012.
However, many Taiwanese remain wary of Beijing's increasing influence over the island. A planned pact to free up the services trade with China sparked an occupation of Taiwan's parliament and mass street protests last year.