Molly, a 45-year-old female elephant, was found lifeless in a rocky river on Tuesday morning, Bali Zoo spokeswoman Emma Chandra said in a statement.
The elephant was being led across the river by a handler Monday to a holding area as part of her daily routine to play and explore when a sudden surge of water carried her away, the statement said.
"Due to heavy rainfall, the river's water level rose suddenly, creating a very strong current. In this situation, Molly lost her balance and was swept away," Chandra said in the statement.
She confirmed to AFP that Molly was a Sumatran elephant and was crossing a river that runs through the zoo.
The zoo launched an overnight search with the help of local residents before Molly's body was found around 6:30 am local time.
"We at Bali Zoo are deeply saddened and grieving the loss of Molly. She was a treasured member of our family and had been with us since 2013," Chandra said in the statement.
Bali Zoo management said they would focus on evacuating Molly's body and preparing for her burial on the zoo grounds.
Torrential rains have battered several Indonesian regions over the past month, causing widespread flooding and landslides.
According to conservation group WWF, Sumatran elephants are on the brink of extinction with only about 2,400-2,800 left in the world.
In the wild, the elephant population is also threatened by rampant poaching because of their tusks, which are prized in the illegal wildlife trade.
Rampant deforestation has reduced the critically endangered elephants' natural habitat and brought them into increasing conflict with humans.
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