Court records show 35-year-old Mickey Joel Paulk is being charged with a state wildlife offence in Alabama.
Paulk has not denied having the pet squirrel, which he named 'Deeznutz', which is illegal under Alabama state law.
But he has denied police allegations that he fed the rodent meth to make it more aggressive.
Officers encountered the animal during a raid at an apartment, with Paulk later stating that he had had the squirrel since it was a baby and "would never give it drugs".
Limestone County sheriff's officers arrested Paulk last week following a chase in which he allegedly rammed an investigator's vehicle.
He now faces illegal gun possession and other charges.