The swap took place last month ahead of Taiwan President Ma Ying-jeou's November 7 meeting with China's leader Xi Jinping -- the first encounter since the rivals split in 1949 at the end of a civil war.
Beijing freed Chu Kung-hsun and Hsu Chang-kuo, the highest-ranking intelligence agents to be jailed in China after they were imprisoned in 2006, Taiwan's Military Intelligence Bureau said.
The release of the pair, who were held on espionage charges, was in exchange for a Chinese double agent, Li Zhihhao, who was jailed by Taiwan 16 years ago under a life sentence.
Unconfirmed media reports in 2013 said China and Taiwan had held talks in Southeast Asia about the exchange of jailed intelligence agents, but that they broke down after Taipei demanded Chu and Hsu be released.
In September a Taiwanese district court sentenced a Chinese man, Zhen Xiaojiang, to four years in prison after convicting him of recruiting local military officers to spy for Beijing.
And in 2011 a Taiwan army general who led an intelligence unit was sentenced to life imprisonment for spying for China, in one of Taiwan's worst espionage scandals.
But the two sides have become closer since Ma's China-friendly government came to power in 2008, pledging to boost tourism and trade links.
However, there is increasing disquiet 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.
And in November, the ruling Kuomintang party was thrashed in local elections, seen as a public backlash over closer ties.
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