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 his colleagues first alerted the government in early May, after they undertook a flight over the delta.
