The recently emerged strain in South East Asia was first reported by Chinese authorities in April this year, and has since been discovered in poultry in Vietnam (August) and Laos (September).
In response the FAO and World Health Organization is calling on countries in Southeast and East Asia, especially those with links to the poultry trade, to be on red alert for signs of avian influenza, and to report any cases.
The FAO is also recommending that governments support poultry producers in the implementation of essential biosecurity measures and standard hygiene precautions.
Juan Lubroth, chief veterinary officer at the FAO, said: "Influenza viruses are constantly mixing and recombining to form new threats.
"However, H5N6 is particularly worrisome, since it has been detected in several places so far from one another, and because it is so highly pathogenic, meaning infected poultry quickly become sick and, within 72 hours, death rates are very high."
According to the FAO, the fact the virus is highly virulent in chickens and geese, and potentially spread across a large area of Southeast Asia, means it poses a real threat to animal health and livelihoods.
The World Organisation for Animal Health (OIE) is also monitoring the situation closely.
Bernard Vallat, director-general, OIE, commented: "An effective surveillance and an early detection of animal disease at source are two main keys to reduce the risk of dissemination and to ensure safe trade. The OIE calls on its 180 member countries to respect their commitment and to immediately notify on WAHIS [the World Animal Health Information System] any outbreak detected on their territory."
So far there has only been one reported case of H5N6 in a human, and the FAO said that while the scientific community is still in the process of understanding the dynamics of the new strain, it is unlikely to represent an immediate and significant threat to human health.