Dr Niall McCann said colleagues in the southern African country had spotted more than 350 elephant carcasses in the Okavango Delta since the start of May.
No one knows why the animals are dying, with lab results on samples still weeks away, according to the government.
Botswana is home to a third of Africa's declining elephant population.
Dr McCann, of the UK-based charity National Park Rescue, told the BBC local conservationists first alerted the government in early May, after they undertook a flight over the delta.
"They spotted 169 in a three-hour flight," he said. "To be able to see and count that many in a three-hour flight was extraordinary.
"A month later, further investigations identified many more carcasses, bringing the total to over 350."
"This is totally unprecedented in terms of numbers of elephants dying in a single event unrelated to drought," he added.