The Forestry Commission said the disease had been identified as affecting larch trees in two woodlands – one in West Sussex and the other in Surrey.
Ramorum is already the most destructive tree disease currently affecting the UK, responsible for the premature felling of more than three million larch trees since it was first confirmed in the west country during 2009.
Most cases have been in the wetter western areas of the UK. This month’s confirmation is the first time it has been recorded so far east, although rhododendron host plants have been previously found to be infected.
Alison Field, south-east England director of the Forestry Commission, said the finding was "bitterly disappointing" but understandable as rhododendron shrubs had been infected near the sites.
"Sadly, the only treatment to prevent this disease from killing millions more larch trees is to fell the infected trees as quickly as possible, before they can produce the spores that can be spread by wind and mist to infect more trees," she said.
The commission’s aerial surveillance team is conducting further flights over the region to check for any further signs of diseased trees.
Ramorum can kill larches within a single growing season, though the timber is still useable after felling. Larch makes up about 5% of British woodland, with about 640ha and 770ha located in Surrey and West Sussex respectively.
The disease is known as "sudden oak death" in the US where it has killed millions of North American native oak and tanoak trees in California and Oregon. The UK’s native oaks have proved more resistant to the disease, with only a handful infected.