The zoo earlier reported that the much-loved hippo, Gustavito, had been stabbed and beaten by unknown assailants.
But prosecutors, who found no sign of puncture wounds, said it was likely the hippo died as a result of poor care.
Gustavito, 15, died late on Sunday.
A detailed examination showed that the animal had apparently died of a pulmonary haemorrhage, or bleeding from the lung, state prosecutor Mario Salazar said.
Earlier reports that Gustavito had been brutally attacked caused international outrage and the alleged incident was described by officials as cowardly and inhumane.
Police later questioned employees of the zoo to try to establish who could have entered the premises to carry out such an attack.
None of the CCTV cameras at the zoo overlook Gustavito's enclosure.
Culture Minister Silvia Elena Regalado said the result of the post-mortem examination did not rule out an attack on the hippo, which she said could have died from the resulting stress.
Following the death, zoo director Vladlen Hernandez said he did not believe employees were involved in any attack and added that the zoo had received no threats from any of El Salvador's feared street gangs.
Mr Hernandez later said that Gustavito had been buried "straight away" because he wanted Salvadoreans to remember the hippo the way he used to be - eating fruit or swimming in his pool.
Last Saturday, the zookeepers noticed Gustavito acting strangely, refusing to eat and unwilling to come out of the pool in his enclosure.
The zoo's veterinarians then reportedly found lacerations on the hippo's neck and face, and the animal clearly in great distress.
His condition worsened on Sunday and he died late that night despite the efforts of the staff to save him.
A post-mortem examination on a hippopotamus at the National Zoo of El Salvador has found that it did not die as a result of a stabbing attack, officials say.