Taiwan's President Ma Ying-jeou said Thursday ties with Beijing will not be affected by his government's probe into a former top negotiator on China policy accused of leaking state secrets.

"Cross-strait relations are like a big tree ... if a pest is discovered we need to find it and remove it so the tree can develop normally. One pest won't affect the development of cross-strait ties," Ma told reporters.

"Since I took office six years ago, cross-strait ties have been systemised step by step and normalised to a certain extent and won't be affected by this incident. Relevant contact and negotiations are still going on."

Ma was asked to comment on the case of Chang Hsien-yao, an ex-deputy minister at Taiwan's Mainland Affairs Council who stepped down earlier this month and is under investigation over allegations he leaked confidential work-related information.

Prosecutors on Thursday reportedly raided Chang's residence and questioned him over suspicions he hid confidential documents at home, reported the United Evening News, citing unnamed sources.

A spokesman at the Taipei district prosecutor's office was not immediately available for comment.

Taiwanese media have reported that Chang is suspected of being a spy for China and allegedly leaked secrets including Taiwan's bottom line in trade negotiations to Chinese officials.

Chang has denied the accusations against him of spying and leaking secrets, and insisted that he followed the instructions of his superiors in dealing with China during his two-and-a-half-year term as deputy minister.

He has alleged that "a few people" risked damaging the improving relations between Taiwan and China by accusing him of being a spy.

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.

However, ties between the former bitter rivals have improved markedly since Ma became Taiwan's president in 2008, leading to the signing of 21 trade and other agreements so far.

The scandal came after China's top official in charge of Taiwan affairs, Zhang Zhijun -- the most senior Chinese official ever to visit the island -- paid a landmark four-day visit in June.

Some observers said Chang's removal could complicate Ma's pro-Beijing push, which has already been hampered by major student-led protests in Taipei against a trade pact earlier this year.