At 69-years-old, she was the country's oldest elephant.
A zookeeper found Hanako lying on the floor of her enclosure on Thursday morning, unable to stand, according to a statement from the Inokashira Park Zoo, where she lived.
Workers tried to get her on her feet to keep her lungs from being pressed under her own weight, but were unsuccessful. She was declared dead later that day, the statement said.
Hanako arrived in Japan when she was two years old, a gift from the Thai government after World War II.
She spent most of her life in captivity as the star attraction at Tokyo's Inokashira Park Zoo but became the center of a growing campaign to improve her living conditions after a picture of her inside her concrete enclosure was featured in a blog post.
"I was shocked and dismayed to see the conditions of her confinement firsthand," wrote Canadian animal rights activist Ulara Nakagawa after she visited the zoo in October.
"Totally alone in a small, barren, cement enclosure, with absolutely no comfort or stimulation provided, she just stood there almost lifeless, like a figurine."
The blog post, featuring a lonesome-looking Hanako, spread on social media and sparked the "Help Hanako" campaign, which proposed that the elderly elephant be moved to a sanctuary in Thailand.
Hidemasa Hori, the zoo's deputy director, told CNN in March that Hanako's confinement was necessary for safety reasons, as she had trampled two people to death in her enclosure in the past.
"It would be better for her to spend the rest of her life here under familiar conditions," he said.