Elephants Without Borders, which is conducting an aerial survey, said the scale of poaching deaths is the largest seen in Africa.
The spike coincides with Botswana's anti-poaching unit being disarmed.
Botswana has the world's largest elephant population, but poachers have been breaching its border.
The scientist carrying out the extensive wildlife survey said many of the 87 dead elephants were killed for their tusks just weeks ago - and that five white rhinos have been poached in three months.
"I'm shocked, I'm completely astounded. The scale of elephant poaching is by far the largest I've seen or read about anywhere in Africa to date," said Dr Mike Chase from Elephants Without Borders.