Taiwan's President Ma Ying-jeou and Chinese President Xi Jinping agreed to set up the hotline between senior officials during a landmark meeting in Singapore in November.
The talks reflected a rapprochement between the two sides since Ma came to power in 2008, but which has stoked fears of growing Chinese influence in Taiwan.
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"Chairman Hsia said in the phone call the hotline is an important concrete outcome from the meeting of the leaders of the two sides. He expects the two sides can communicate more smoothly in urgent matters through the hotline," the statement said.
It described the hotline as "another important step forward" in exchanges between China and Taiwan.
Ma Xiaoguang, spokesman for China's Taiwan Affairs Office, confirmed the call had taken place, Beijing's state news agency Xinhua reported.
"We hope the two authorities will make efforts to maintain and promote peaceful development of cross-Strait relations," Xinhua quoted Ma as saying.
November's summit was the first time leaders from the two sides had met since their traumatic 1949 split.
No agreements were announced between the two, which still refuse to formally recognise each other's legitimacy, and Ma Ying-jeou's participation faced significant opposition at home.
Tensions between Taiwan and China have decreased markedly since Ma, of the China-friendly Kuomintang party, (KMT) came to power promising to beef up trade and tourism links.
But public sentiment in Taiwan has recently turned against closer ties with Beijing, with voters saying trade deals have been agreed in secret and have not benefited ordinary citizens.
The KMT suffered its worst-ever showing in local polls last year and is tipped to lose in the presidential election in January.
China and Taiwan split at the end of the civil war on the mainland in 1949, and Beijing still regards the island as a province awaiting reunification, never ruling out the use of force to achieve it.
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