The panda was initially set to head to China in 2021 but its departure was postponed multiple times due to travel restrictions linked to the pandemic.
In Wakayama, visitors came to say good-bye to Eimei, which became the world's oldest to father a baby panda in 2020 at age 28, the equivalent of being in his 80s for a human, as well as his twin daughters.
"Everyone is so cute I almost cried," a woman in her 70s told public broadcaster NHK.
"I'm sad they're going back to China."
The black and white mammals are immensely popular around the world and China loans them out as part of a "panda diplomacy" program to foster foreign ties.