Described as "Africa's last Eden, " it draws thousands of visitors annually.
"We started flying the survey on 10 July, and we have counted 90 elephant carcasses since the survey commenced", Mike Chase, the charity's director, said.
The latest killings have been found deep into Botswana - close to the protected Okavango Delta wildlife sanctuary, which attracts tourists from around the world. The census found roughly 350,000 elephants in 18 African countries.
Prior to the recent incident, Botswana had been largely "successful at protecting [its] elephants", according to the Great Elephant Census, an expansive survey released by Elephants Without Borders in 2016.
It is understood that 87 of the elephants were poached for their tusks, with five white rhinos also slaughtered in the last three months.
"The varying classification and age of carcasses is indicative of a poaching frenzy which has been ongoing in the same area for a long time", the report says.
Poachers had attempted to hide the "mounds of rotting flesh" with drying bushes, the report said.
Conservationists fear the final figure of poached elephants for the year will only increase and are concerned the problem is being ignored as it is bad for the country's reputation.
Then, this May, President Carter Morupisi issued a directive stripping the guns from anti-poaching units patrolling the country's porous border regions.
While the move may have alleviated tension with Botswana's neighbours, conservationists believe it could be providing an opening to emboldened ivory traffickers.
Data from elephant tracking collars shows elephants enter Botswana from neighboring Angola, Namibia and Zambia where they were at more risk of being poached.
A ban on commercial trade in ivory across worldwide borders went into effect in 1990, but many countries continued to allow the domestic buying and selling of ivory. "That is one of the reasons why, in Botswana, with our anti-poaching unit, we don't necessarily interrogate the poacher".
The recent developments may affect the remaining elephants negatively unless the Botswana government takes action to preserve its reputation as an elephant sanctuary.
'Our new president must uphold Botswana's legacy and tackle this problem quickly.