India says nearly 18,000 horses have contracted equine influenza and 16 have died.
In a report to the World Organisation for Animal Health (OIE), India says the outbreak has occurred in Jammu and Kashmir, the country's northernmost state.
The report put the date of the first outbreak, in the village of Katra, at June 20 and the second, centred on the village of Anantnag, as beginning on July 7.
Both villages are close to the Pakistan border.
The report does not make clear whether the outbreaks are resolved, but recent reports out of India suggest cases are continuing to occur.
The OIE said in addition to Anantnag, several other districts are affected: Budgam, Pulwama, Srinagar, Kupwara, Baramula.
India says most of the affected horses are used for transport and that movement controls and screening measures have been put in place.
The outbreak is known to have disrupted the horse racing programme in several areas.
Vaccine is not being used.
The Katra outbreak resulted in 15 horse deaths while just one horse has reportedly died in the Anantnag outbreak.
Earlier unofficial estimates had put the number of cases at about 5000.