In recent weeks, Ling Ling, who was 22, had lost his appetite, moved slowly and "had a swollen face and abdomen, indicating gradual organ failure," the Yomiuri Shimbun newspaper said.
His death came just one day after the Ueno Zoo had withdrawn him from public view. Japanese TV showed visitors writing messages of condolence, and decorating his enclosure with flowers and bamboo.
The panda was born in Beijing Zoo and came to Tokyo in November 1992 as a gift by China to Japan to commemorate the 20th anniversary of normalized relations between the two countries.
Ling Ling was the only giant panda owned by Japan. The country has eight other pandas, but all of them are on loan from China.
Beijing has often presented giant pandas, reared in its southwestern province of Sichuan, to foreign countries as a way of marking good relations. However, last year national media reported that the country was set to end its 'panda policy' and would only loan them in future for breeding and biological research.
Chinese President Hu Jintao is set to arrive in Japan next week on the first visit by a Chinese leader to the country in 10 years, and the issue of a new panda loan might be raised.
The visit comes amid improving relations between Tokyo and Beijing. Relations had earlier been soured due to former prime minister Junichiro Koizumi's repeated visits to the Yasukuni Shrine in Tokyo, seen as a symbol of Japanese militarism, and Japan's reluctance to apologize for massacres in the occupied part of China during WWII.
