Xinhua reported that Mongolia's vice premier, M. Enkhbold, called a state emergency situation committee meeting on Monday to consider the response to the epidemic.
Just three provinces - Bayan-Ulgii, Zavkhan and Umnugobi - are unaffected at this stage.
The government is reported to be considering promoting vaccination.
Mongolia has experienced several equine flu outbreaks in recent decades.
Outbreaks in Khovd province in 2007 and 2008 caused big losses to the local livestock industry.
Mongolia has an estimated two million horses.