Common frogs, which are the most widespread species of frog in Britain, have suffered declines of around 80 per cent in the areas worst hit by the disease, known as ranavirus.
Research by biologists at the Zoological Society of London also fear that the virus could be having an equally devastating effect on other native amphibians found in the UK including the common toad and smooth newts.
Dr Trent Garner, a senior research fellow at the Institute of Zoology at the Zoological Society of London, said: "Many of these populations are hanging on by a handful of frogs.
"If the disease causes the frog populations to fall so low then so many other factors come into play that could cause local extinctions."
"Ranavirus disease has sort of fallen under the radar but it has been a problem in many parts of the world for decades.
"Many of the die offs we receive reports about are in garden ponds and you get really sad accounts of all the frogs in a pond dying out."
The researchers examined frog numbers in a selection of populations around the country where ranavirus disease had been previously reported since 1996.
They found that in half of the populations they looked at, there had been repeated outbreaks of the disease. In almost a quarter of the cases, frog numbers had dropped by more than 80 per cent.
Ranavirus is first thought to have appeared in Britain in the 1980s when the first deaths were reported in the South East of England after being introduced through imported fish or amphibians.