“I hope my trip will be conducive to the peaceful development of the two sides and enhance Taiwan’s security as well as people’s economic well-being,” Wu told reporters before leaving Taiwan.
Tensions between the two sides have shown signs of easing after Taiwan‘s independence-leaning Democratic Progressive Party was defeated in the March presidential poll.
Ma was sworn in as president on May 20.
Ma has pledged to seek economic engagement with China while building closer trade and tourism links.
The two sides last held talks in 1995 but China suspended further discussions to protest against a visit to the US the same year by Lee Teng-hui, Taiwan‘s then president.
The eight-year presidency of Chen Shui-bian, Ma’s predecessor, was marked by confrontation with Beijing.
China accused Chen of seeking formal independence for Taiwan.
China demands unification with the self-governed island and has threatened to attack if Taiwan seeks a permanent break.
The Nationalist Party fought a bloody civil war with the Chinese communists on the mainland, and their defeated forces fled and resettled in Taiwan in 1949.
During Wu’s five-day visit, he is expected to visit a Buddhist temple in the eastern Chinese province of Jiangsu, to pray for victims killed by the earthquake in Sichuan.
Taiwan has sent a rescue team to southwest Sichuan province to help tackle the aftermath of the devastating earthquake there, which has killed more than 65,000 people.