Police were called to the Alley Pond Environmental Center in Douglaston Monday after employees discovered that the reptile, named Millennium, was gone.
Authorities say its enclosure had been broken, and the NYPD confirmed there was a forced entry.
Investigators are searching for surveillance video footage. Millennium weighs approximately 90 to 95 pounds, and he is described as a gentle giant known for eliciting smiles and laughter from kids and a love of watermelon.
Handlers believe whoever took him is likely in over his or her head.
"He's two-and-a-half-feet long by two-feet-wide by one-foot-tall," one worker said. "He's a very strong turtle you just can't have in a home."
Mini Me has lived with Millennium for more than a decade, and authorities have not been determined why the thieves stole one animal but not the other.
"Are they going to be able to maintain the turtle properly, feed him the proper food and properly care for him?" the worker asked. "That's my biggest concern."
With each passing minute Millennium spends away from the habitat he's called home, fear and anxiety are growing among those who love him.
"To me, the turtle is priceless for a big animal like that, and so many kids love him," the staffer said. "He's priceless. The retail value out there, I don't know, from several hundred to several thousand. Who knows?...no questions asked, you can walk away, just bring the turtle back to make sure he's well taken care of."
Alley Pond is a nonprofit educational organization that advocates for sustainable environmental policies and practices.
Anyone with information is urged to contact police.