News of Peanut’s death came as a petition calling for his return had garnered more than 30,000 signatures by Friday afternoon.
On Thursday, Mr Longo had said he was raising money for legal fees against the DEC. A GoFundMe he set up had raised about $13,500 (£10,400).
The ordeal, he said in a Friday morning post, had become a “terrible nightmare”.
After Peanut’s death, Mr Longo posted the phone number of the DEC online and urged supporters to call the organisation to “express your feelings”.
“We will not let this be Pnuts final memory,” he wrote.
In a separate Instagram story, he thanked Peanut’s fans for the “love and support” his family had received and called for donations to help other animals kept in his “freedom farm”.
A DEC statement said an investigation had been launched after receiving “multiple reports from the public about the potentially unsafe housing of wildlife that could carry rabies and the illegal keeping of wildlife as pets”.
Mr Longo took Peanut in seven years ago after he spotted the baby squirrel by his mother, who had been hit by a car.
He cared for Peanut until he was strong enough to be released, but said he found the critter back on his porch the following morning with “a chunk of his tail missing”.
Peanut’s Instagram account has amassed more than 500,000 followers in the time since.
The account features videos of Peanut playing out skits with Mr Longo, occasionally dressed in hats, often climbing over him or being hugged, and regularly eating waffles.
(Except for the headline, this story has not been edited by PostX News and is published from a syndicated feed.)