Gustavito, a 15-year-old hippopotamus who had been in the National Zoological Park in eastern San Salvador almost all his life, died February 26 after suffering for days.
The government, giving information from the zoo, said the hippo had been stabbed and beaten by unidentified assailants four days earlier, resulting in internal bleeding.
That account triggered shock and revulsion in the Central American nation and was relayed in international media reports.
But the autopsy revealed no puncture marks in the animal's 2.5-centimeter (1-inch) thick skin, state prosecutor Mario Salazar revealed on Thursday.
Instead a detailed forensic examination showed Gustavito had apparently died from pulmonary hemorrhaging - acute bleeding from the lung.
The culture minister, Silvia Elena Regalado, said that in itself did not rule out an attack on the hippo, which she said could have died from the resulting stress.
But a workers' union in her department had said that the hippopotamus had been ill for 17 days before its death, and alleged that authorities had not properly followed up on the matter.
The head of the environmental activists' group UNES, Mauricio Sermeno, said the initial account of a deadly attack on the big hippo "was something unbelievable."
The government should "publicly apologize and give the true version of the death," he said.
He also advised against closing the zoo, as some critics have called for in the wake of the hippo's demise.
"The zoo is in a precarious position, with insufficient resources," Sermeno said. "What could be done is to restructure the park and give it more support so it can maintain the species" he said.
