He declined to specify a number. Tests are underway to determine the exact cause of death.
The six villages are in the northeast of Crimea, in the same region as five towns that had previously reported the death of some 2,500 poultry from avian flu.
Kyiv declared a state of emergency on 3 December in an effort to contain the spread of the infection.
The birds are thought to have contracted the virus from wild birds using the nearly Sivash saltwater lake as a stopover or wintering site.
It is not known yet if the virus in Ukraine is the H5N1 strain responsible for the death of at least 68 people in Asia since 2003.