Taiwan on Monday named a new minister for China affairs in an attempt to reboot cross-strait relations after a row over espionage and growing anxiety about Beijing's influence on the island.

Deputy defence minister Andrew Hsia succeeded Wang Yu-chi as the chairman of the Mainland Affairs Council, which handles relations between Taipei and Beijing, after Wang resigned last week.

Wang had accused a former deputy minister at the council, Chang Hsien-yao, of leaking confidential documents to Beijing.

However prosecutors decided not to indict Chang, who has vehemently denied the claims, saying there was not enough evidence to do so.

An angry Wang ridiculed the decision but resigned his post anyway, saying he had to accept political responsibility.

His replacement Hsia had been a career diplomat before he was appointed a deputy defence minister in October 2013.

Authorities in both Beijing and Taipei have stressed that cross-strait ties will not be affected by the espionage allegations.

Taiwan and China split in 1949 after a civil war, although Beijing still considers the self-ruled island part of its territory awaiting reunification, by force if necessary.

Ties between the two have improved markedly since Ma Ying-jeou of the China-friendly Kuomintang party came to power in 2008. He was re-elected in 2012 as the president.

However, the public has grown increasingly anxious over China's influence on the island.

Taiwan last month slammed a unilateral move by China to open four new flight routes over the strait between them as "unacceptable", saying it risked allowing planes to fly too close to aircraft on existing routes

A proposed trade pact with the mainland sparked mass student-led protests and a three-week occupation of Taiwan's parliament last year.

In November, the Kuomintang was routed in local elections seen as a public backlash over the warming ties.