"The crocodile was found dead on Sunday," regional water management official Vangelis Mamangakis told AFP.
"It will be taken to the natural history museum of Heraklion for tests," he added.
Nickhamed Sifis -- Cretan for Joseph -- the Nile crocodile had assumed nationwide notoriety after being discovered last summer at an artificial lake.
The fearsome two-metre reptile was last seen in mid-February, Mamangakis said, adding that an initial veterinary inspection had pointed to death from cold exposure.
Crowds had flocked to the lake last summer to catch a glimpse of the animal, whose appeal only increased when it repeatedly eluded attempts to trap it.
Local officials say the beast had likely been abandoned by its owner up to two years ago.
The Crete crocodile is not the first to make an unexpected appearance in European waters. In 2001, fire officers in Austria were called to rescue from the Danube a South American crocodile, which was later taken to a Vienna zoo.
