One of Taiwan's top negotiators on China policy has resigned and is under investigation over suspicions related to "national security", authorities said Tuesday.

The row at the Mainland Affairs Council which handles cross-strait relations could upset President Ma Ying-jeou's push for closer ties with China, analysts said.

The council initially announced that Chang Hsien-yao, the deputy minister for mainland affairs, had stepped down over the weekend for family reasons.

However Chang cried foul, telling reporters he had been ordered to quit amid unspecified allegations against him which he branded as "concocted".

The row took another twist Tuesday when the council said that the Investigation Bureau, which is tasked with countering Chinese espionage as well as criminal activity, had launched a probe into Chang.

"Since part of the suspicion regarding Chang's work has been related to national security, we decided to transfer the case to the Investigation Bureau for further investigation," council spokeswoman Wu Mei-hung told reporters.

She would not be drawn on details of the concerns, saying only that the council's move was prompted by a recent tip-off.

Local media suggested Chang might have leaked classified information during previous talks with China.

The United Daily News quoted an unidentified government official as saying the investigation could be connected with "leaking secrets" including the bottom line in negotiations.

Chang rebuffed the allegations in comments on a pre-recorded talk show. Cable news network TVBS released some of the footage before the show is broadcast late Tuesday.

"I knew too many things, some of them I felt were improper and made frank suggestions. Maybe my suggestions made some people unhappy," he argued.

Chang compared the investigation against him to being hunted down by a "mafia".

"I've written down everything in my will, I've made preparations," he said, wiping away tears.

Ties between Taiwan and China have improved markedly since 2008 when Ma of the China-friendly Kuomintang party came to power.

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.

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

"The incident might have a negative impact on cross-strait ties, when mutual trust between the two sides is fragile," said Chang Ya-chung, a professor at National Taiwan University.