In addition to the 2,000 dead, another 10,000 are believed to be infected, Ohad Hatsofe, a specialist at the Israel Nature and Parks Authority, told AFP.
The virus affects Israel annually, but this year’s outbreak is much larger than previous years, said Uri Naveh, a senior scientist at the authority.
Naveh described the number of dead cranes as “exceptional”.
Like every year, roughly 100,000 wild cranes reached Israel since October, most stopping in the Hula Valley, an important point on their migratory path towards Africa.
More than 40,000 cranes are estimated to have remained in the area.
The avian flu ravaging the population, H5N1, has been detected in some chicken populations in northern Israel, Israel’s agriculture ministry said.
The ministry has suspended egg sales from affected farms.
It is rare for H5N1 to spread among humans, but there have been past outbreaks.
According to the World Health Organization H5N1 has killed more than 450 people, mainly in Indonesia, Egypt and Vietnam, since 2003.