Welfare group In Defense of Animals India, which has been working for the welfare of working horses for the past three years, saw the first cases there in the first week of October.
"A couple of cases were presented for respiratory problem and high temperature," said Dr P M Bhosale and Dr Amit Sharma in a report on the welfare group's website.
"Attributing it to change in climate, they were treated accordingly," they said. "But soon more and more cases presented with similar symptoms."
The group realised they were facing an equine influenza outbreak and provided medical care for the growing number of sick horses, which ultimately numbered more than 400.
"The equine welfare team of IDA India worked from dawn till late night so that all the animals could be attended. Parallel to this, they started counseling the guardians about preventive measures to be taken.
"All the movement of horses in and out of Matheran was restricted to avoid spreading of disease to virgin territories. Guardians were asked to provide adequate rest to animals till full recovery and isolation of affected animals from the healthy ones."
Many of the horses were used in the transport of tourists.
"Their persistent efforts, dedication and promptness to deal with the outbreak resulted in zero mortality and minimal suffering."
Government authorities were also involved in treating the outbreak.
However, suspected cases reported in the Mumbai region in recent days indicate the highly contagious virus may have spread.