The first deaths were reported in early May in the Okavango Delta.
Dr Niall McCann, director of conservation at UK-based charity National Park Rescue, told the Guardian: “This is a mass die-off on a level that hasn’t been seen in a very, very long time.
“Outside of drought, I don’t know of a die-off that has been this significant.”
Poisoning or an unknown pathogen are thought to be the most likely causes.
The tusks of the elephants have not been removed by poachers.
Seventy percent of the deaths were around waterholes, according to local sources.
Some of the animals were spotted walking in circles, a sign of neurological impairment.
Dr McCann said: “If you look at the carcasses, some of them have fallen straight on their face, indicating they died very quickly.
And a number of other elephants appear to be weak sparking concern they could also die.
Dr McCann criticised the Botswana government over the testing of samples.
He said: “When we’ve got a mass die-off of elephants near human habitation at a time when wildlife disease is very much at the forefront of everyone’s minds, it seems extraordinary that the government has not sent the samples to a reputable lab.
“There is no precedent for this being a natural phenomenon but without proper testing, it will never be known.”
The Okavango Delta is home to around 15,000 elephants, 10 percent of Botswana’s total.
Dr McCann said: “You see elephants as assets of the country. They are the diamonds wandering around the Okavango Delta.
“It’s a conservation disaster – it speaks of a country that is failing to protect its most valuable resource.”
Dr Cyril Taolo, acting director for Botswana’s department of wildlife and national parks, told the Guardian: “We are aware of the elephants that are dying.