Botswana has previously had a zero-tolerance approach to poaching, with a "shoot-to-kill" policy against poachers.
The number of African elephants has fallen by around 111,000 to 415,000 in the past decade.
The killing continues at a dizzying pace of about 30,000 elephants a year to meet demand for ivory in Asia, where tusks.
Ninety elephant carcasses have been discovered in Botswana with their tusks hacked off, a charity said Tuesday, in what is believed to be one of Africa's worst mass poaching sprees.
Most of the animals killed were large bulls carrying heavy tusks, Elephants Without Borders said.
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 started flying the survey on July 10, and we have counted 90 elephant carcasses since the survey commenced," Mike Chase, the charity's director, told AFP.
"Each day we are counting dead elephants," he added.
The wild pachyderms were shot with heavy-calibre rifles at watering spots near a popular wildlife sanctuary in the Okavango Delta.
According to Chase, the carcasses' skulls were "chopped open by presumably very sharp axes, to remove their tusks". In some cases the trunks were also removed.
"The scale of elephant poaching is by far the largest I have seen or read about in Africa to date," Chase said, adding that the poaching coincided with Botswana's rangers being reportedly disarmed earlier this year.
Botswana has previously had a zero-tolerance approach to poaching, with a "shoot-to-kill" policy against poachers.
The landlocked country with its unfenced parks and wide open spaces has the largest elephant population in Africa at over 135,000.
Chase said elephants in Zambia and Angola, north of Botswana, "have been poached to the verge of local extinction, and poachers have now turned to Botswana".
Botswana Tourism Minister Tshekedi Khama confirmed to AFP that dozens of elephants had been poached.
"I am very concerned, it's a huge worry," he said. "I'm aware that the numbers are in double digit, and for Botswana they are high.
"Because we had been spared poaching for a long time, I think now we are realising the sophistication of these poachers.
"Unfortunately sometimes we learn these lessons the hard way," he said.
Defence chief Major-General Placid Segokgo told AFP that he was unable to immediately comment on rangers being apparently disarmed earlier this year under a new government policy.
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).
The killing continues at a dizzying pace of about 30,000 elephants a year to meet demand for ivory in Asia, where tusks sell for around $1,000 a kilo.
The Botswana poaching occurred just months after former president Ian Khama, deeply passionate about protecting wildlife, stepped down, handing power to his chosen successor Mokgweetsi Masisi.
Global conservationist International Fund for Animal Welfare (IFAW) expressed shock at the slaughter.
"Until now Botswana's elephant herds have largely been left in peace, but clearly Botswana is now in the cross-hairs," said Jason Bell, IFAW's vice president for conservation.
Poachers have also targeted rhino in Botswana, after six white rhino carcasses were found in recent months.