The elephant had been carrying 200 pounds of ivory in its tusks, and was the largest to be hunted in the country since 1996.
"Her death was shocking ... because she looked fine after being amputated and actively moving," said Rika Marwati, a veterinarian.
The men now face up to 20 years in federal prison after being indicted on 11 federal charges.
Demand for the endangered species in the Philippines has been fueled by the clampdown on the ivory trade.
African elephant numbers have fallen dramatically as a result of poaching and other factors, such as habitat fragmentation or loss.
Prehistoric Europeans used amber as a status symbol, an archaeologist who worked on the study told Newsweek.
The operation seized thousands of animals and identified around 1,400 people suspected of related criminal activity.
The Kenyan official made the statement during Sudan's, the world's last male northern white rhino, funeral on Saturday.
'Kenya is making a statement that for us ivory is worthless unless it is on our elephants,' President Uhuru Kenyatta said.
As many as 50,000 elephants are killed each year for their tusks.
The event is designed to raise awareness about the poaching epidemic of African elephants.
More than 20,000 African elephants were killed for ivory in 2013, and Thailand imports a lot of that.