Wild horses in the Greater Alpine National Park.
In 2009, feral horse numbers in the surveyed areas had rebounded to 7679 animals, it said, adding that there was margin of error of plus or minus 25.4 per cent.
"The estimated increase in the feral horse population between 2003 and 2009 was 324 per cent," it said.
This translated to an estimated average annual rate of increase 21.65% - very close to the maximum reproductive rate of around 20 per cent scientifically predicted for the alpine area.
"If the feral horse population continues to grow at this rate, it is predicted it will reach around 13,800 feral horses in 2012," the parks department said.
It said brumbies had lived in the Australian alps for more than 150 years after escaping from early settlements.
"The close link between wild horses and the European culture of the Australian Alps is well recognised. But 150 years of horse escapes and breeding have resulted in the large number of feral horses that currently occur in the Kosciuszko National Park in New South Wales, the Alpine National Park in Victoria and adjacent areas of state forest in both jurisdictions."
The department said wild hroses are considered a significant threat to the natural values of the Australian Alps because of their impacts, widespread distribution, and the challenges involved in their management.
"Horses have significant impacts on streams in particular stream banks in the Australian Alps.
"In alpine and sub-alpine areas, threatened species such as corroboree frogs, the broad-toothed rat, the alpine water skink and bog skink and a variety of plants are at risk from feral horse impacts," it said.
"Feral horses present a complex management problem because they have emotional and historical significance to many people; and effective and acceptable control methods are yet to be identified to match the growth in feral horse numbers.
"It is likely that the impacts of feral horses on alpine and sub-alpine communities - particularly wetlands, karst areas and peatlands - will become more widespread and more intense without a substantial reduction in the number of feral horses in the Australian Alps."
Removal rates by current techniques would need to increase many-fold to match the current and projected population increases, it said.
"Improved control techniques will need to align with community expectations for humane removal, and also increase the number of feral horses removed from national parks."
"The cultural significance of horses within the community must be balanced against the effects of feral horses on the environment. Left unchecked, horse numbers have the potential to further degrade one of Australia's most significant and sensitive environments."