"We found a highly pathogenic avian influenza sub-type H5N1 (virus) with clade 2.3..." the agriculture ministry's veterinary chief Syukur Iwantoro said in the letter obtained by AFP.
"This clade is a new clade found for the first time in Indonesia, that is very different to the avian influenza found before, which is clade 2.1."
A clade is a group of organisms, usually species, with a common ancestor.
A poultry breeders' association had reported the death of more than 300,000 ducks in several provinces on Java island since November to the ministry.
The veterinary office found the H5N1 virus involved was a different clade to that usually found in Indonesia, said Iwantoro's letter to local government offices and the World Health Organisation (WHO).
Iwantoro called for further research into whether there had been a genetic shift in the virus previously found in the country, or whether the new strain originated overseas.
"There is a suspicion that the virus has spread from other countries, possibly from Vietnam or Thailand," Emil Agustiono, secretary of the National Commission of Zoonosis Control that oversees bird flu, told AFP.
Health officials have told local governments to stop and check motorbikes and pick-up trucks commonly used to transport poultry, to try to reduce the spread of the virus.
The health ministry has told local offices to be vigilant of more massive poultry deaths, or for deaths of people in the vicinity, its head of communicable disease Tjandra Yoga Aditama told AFP.
Bird flu typically spreads from birds to humans through direct contact, but experts fear it could mutate into a form that is easily transmissible between humans.
Indonesia has suffered the world's worst human fatalities from bird flu with 159 deaths since 2003 out of 359 worldwide, according to the WHO.