Investigators believe Escalera disposed of the paint by dumping it in the hole.
Several days later, a couple driving on County Road 455 spotted the tortoise crossing the road and took it to an animal sanctuary for help.
Experts said the paint could have affected the tortoise in many ways, including disrupting his heat regulation and causing poisons to leach into his body, as well as destroying his natural camouflage protection.
Escalera, who said he didn't know the gopher tortoise was in the hole, was charged with littering and with injuring the endangered gopher tortoise.
Charges were filed through the state attorney's office, so an arrest was not immediately made. The company declined to comment.
CAPE CANAVERAL, FL - DECEMBER 07: A Gopher Tortoise crawls near the Space Shuttle Atlantis at the Kennedy Space Center December 7, 2007 in Cape Canaveral, Florida. NASA continues to evaluate sensor issues. Atlantis is re-scheduled to launch tomorrow December 8, 2007 for a mission to the International Space Station. (Photo by Eliot J. Schechter/Getty Images)