According to Elephants Without Borders, the scale of the deaths is the largest in Africa.
The Elephants Without Borders group and wildlife officials in Botswana have conducted half of a national elephant census and so far have counted almost 90 "fresh and recent" carcasses of poached elephants, group director Mike Chase said in an email.
The recent developments may affect the remaining elephants negatively unless the Botswana government takes action to preserve its reputation as an elephant sanctuary.
'The poachers are now turning their guns to Botswana.
The scientist carrying out the survey said numerous elephants were killed for their tusks just weeks ago and that five white rhino have been poached in three months, according to the report.
Botswana has the world's largest elephant population standing at 130,000 and over the years many have moved from neighbouring Angola, Namibia and Zambia to stay.
Those conditions could include a dearth of elephants to kill after widespread poaching, or crackdowns on trafficking syndicates in some cases. The wide variety of classification and age of the dead elephants indicated a "poaching frenzy" that "has been ongoing in the same area for a long time".
The grim discovery was made over several weeks during an aerial survey by scientists from Elephants Without Borders and Botswana's Department of Wildlife and National Parks.
"We have the world's largest elephant population and it's open season for poachers", said Dr Chase.
"Until now Botswana's elephant herds have largely been left in peace, but clearly Botswana is now in the crosshairs", said Jason Bell, IFAW's vice president for conservation.
The number of African elephants has fallen by around 111,000 to 415,000 in the past decade, according to the International Union for Conservation of Nature (IUCN).
'Our new president must uphold Botswana's legacy and tackle this problem quickly. "Tourism is vitally important for our economy, jobs, as well as our global reputation which is at stake here as being a safe stronghold for elephants".
"A month after you were sworn in you disarmed the anti-poaching unit".
Shockingly, the mutilated elephants were found near the protected Okavango Delta region, and far away from the borders where poaching has traditionally been more rife.