The emergence of the toxin, produced by a cyanobacteria, could be due to a severe drought previous year followed by good rains this season, said Cyril Taolo, deputy director of the department.
The three affected countries had previously - until now - doubted that the bacteria was to blame for the death of the elephants, primarily because standing water algae is found on edges or sides of ponds and not in the middle where elephants drink from.
Hundreds of elephants that died mysteriously in Botswana's famed Okavango Delta succumbed to cyanobacteria poisoning, the wildlife department revealed on Monday.
Taolo said that the specific type of neurotoxin had yet to be established and that, for now, there was no evidence to suggest that Botswana's wildlife was still under threat as the deaths appear to have ceased.
Cyanobacteria occur commonly in water, but those that produce toxins are becoming more common due to climate change, officials said. Both male and female elephants of all ages died, with clinical signs limited to neurologic symptoms, said Taolo.
He, however, could not explain why these toxins did not affect any other animals drinking the affected water.
The spate of deaths ended in late June, coinciding with the drying up of pools of water where cyanobacteria contamination would have taken place.
The department's principal veterinary officer Mmadi Reuben told the same conference that there were, however, still many unanswered questions. Because of climate change, Southern Africa's temperatures are rising at twice the global average, scientists say.
Featured image: A dead elephant is seen in this undated handout image in Okavango Delta, Botswana May-June, 2020. It did not mention evidence from Africa, but cited examples from many other countries worldwide, saying that the toxic blooms can kill or injure fish, birds and mammals. Parks authorities believe the elephants could have ingested the bacteria while searching for food. But Botswana, home to nearly a third of the continent's elephants, has seen numbers grow to around 130,000. The carcasses were found near water sources.
While Africa's elephant population is decreasing due to poaching, Zimbabwe, South Africa, Botswana and Namibia unsuccessfully lobbied for the Convention on International Trade in Endangered Species in August for controlled sales of their ivory stocks.