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The location was about 500 feet from the tortoise enclosure where Abu escaped Aug. 1.
The zoo said the father and son will receive the promised $4,500 reward officials offered for information about the missing animal's whereabouts.
"I feel relieved. From now on, we'll make sure to take perfect care of our animals," zookeeper Yoshimi Yamane told The Japan Times.
Yamane said the tortoise was found uninjured and healthy.
She said the tortoise "is now being given plenty of food to eat."
Another zookeeper at the facility suggested Abu may have taken a longer journey than her location Wednesday might imply.
"She might have climbed a mountain, making a big detour," the keeper told The Asahi Shimbun.