Taiwan's China affairs minister Wang Yu-chi resigned Tuesday after prosecutors decided not to indict a former deputy whom he had accused of spying for Beijing.

Wang had alleged in August that Chang Hsien-yao, a deputy minister at the Mainland Affairs Council which handles relations between Taipei and Beijing, was leaking national secrets to China.

Chang vehemently denied the allegations, but stepped down from his post in August of last year, and prosecutors launched an investigation into the claims.

He was cleared Tuesday after authorities said there was not enough evidence against him.

"I disagree with the reasons of the prosecutors that enabled them to make the decision," Wang, the council's chairman, told reporters.

He said however that he had to respect it, stating: "I would like to resign to take responsibility."

The government has yet to announce who will take over from Wang.

Chang was not immediately available for comment Tuesday.

He has previously told reporters he was ordered to quit over the unspecified allegations against him, which he branded as "concocted", even comparing them to being hunted by a "mafia".

He has insisted that he followed the instructions of his superiors in dealing with China during his two-and-a-half-year term as deputy minister, and had pledged to cooperate with the investigation to clarify the truth and clear his name.

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 2008, however, when Ma Ying-jeou of the China-friendly Kuomintang party came to power. He was re-elected in 2012 as the president.

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

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.

Ma has said ties with China will not be affected by Chang's case.