The 15-year-old mammal suffered "multiple blows on different parts of the body" from "blunt and sharp objects" in Wednesday's attack, the Ministry of Culture said in a statement.
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Vets found lacerations on the hippo's neck and face, and the animal clearly in great distress.
The San Salvador zoo said experts had been caring for the animal around the clock since discovering he had been attacked but he succumbed to his injuries on Sunday.
Gustavito was a much-loved resident of the zoo
The zoo plans to perform a necropsy to determine the exact cause of death.
Director Vladen Henríquez said Gustavito also had injuries to his feet and wounds on his cheek that could have been caused by an ice pick.
Protesters demonstrated against the hippo's murder
"There were injuries inside his mouth," Henríquez said, adding that they were probably inflicted "when the animal tried to defend himself."
Officials said they found pieces of metal and rocks inside the hippo's enclosure.
Floral tributes left for Gustavito
Police are searching for the killers and the motive for the attack remains unclear.
"We are outraged and saddened over the killing of the hippopotamus," said Culture Minister Silvia Regalado.