Taiwan has been negotiating with China to swap spy agents jailed on both sides despite improving ties, the island's defence minister said Wednesday.

"It is a very important task for us to (swap) the fallen colleagues. We are working on this through the channels we can utilise," Kao Hua-chu said when asked about the matter in parliament.

He said the Mainland Affairs Council, Taiwan's top China policy-making agency, and the semi-official Straits Exchange Foundation are negotiating with the relevant Chinese authorities, but did not elaborate further.

Taiwan and China have spied on each other ever since they split in 1949 at the end of a civil war. Beijing still regards the island as part of its territory awaiting reunification, by force if necessary.

Despite the underlying tension, the two sides have seen significant progress since 2008 after Ma Ying-jeou of the China-friendly Kuomintang party became Taiwan's president.

But Ma has said that Taiwan should strengthen its defences against Chinese espionage, following a string of spy scandals that showed intelligence gathering has continued despite warming ties.

Taiwan's military court earlier this year handed out life sentences to an army general and an intelligence officer for spying for China in the island's worst espionage scandals in recent years.

The general was allegedly lured in a honey trap by a Chinese female spy to gather information for Beijing while the officer reportedly had helped China unravel several of Taiwan's spy networks on the mainland.

A retired Taiwanese agent recently warned that at least 10 Chinese moles were believed to have infiltrated the island's security units.