The ACT Government has begun a premature harvest of tens of thousands of pine trees in Kowen Forest, after they were damaged by a rare chain of events.

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For months locals have been mystified by growing areas of dieback near the Molonglo Gorge nature reserve, east of Canberra.

Bungendore resident Bob Nicoll drives along the Kings Highway and past Kowen Forest daily. At first he noticed a small area of damage but as the weeks went on, more and more trees began to die.

"Instead of being the normal pine forest green, there started to be a lot of dead and dying trees," Mr Nicolls said.

"I asked people around Bungendore why and nobody knew."

The professional geologist said he needed to get to the bottom of the dieback.

"As a scientist... you are aware of the environment, and to see a large area of trees dying off, you think there must be some cause behind it."

Freak storm partly to blame

The aftermath of a severe hailstorm in Queanbeyan, 11 February 2016. ( ABC News: Greg Nelson )

ACT Forestry coordinator Peter Langdon said it comes back to a freak hailstorm that lashed the Queanbeyan district back in February.

The supercell dumped hail stones the size of golf balls in the forest and caused significant property damage in Queanbeyan itself.

"It was a severe hail storm, so large hail stones and a lot of them," Mr Langdon said.

"It's stripped the bark off the tender shoots of the trees and knocked out and damaged the growing tip of the pine tree, which is essential for growing a single straight saw log."

While the trees could have recovered, he said the final blow was a naturally occurring fungus.

"It's (the storm damage) allowed diplodia fungi, which was present at low levels within the radiata pine, to enter into the tree's system and attack the tissue of the plant, killing many of the trees and preventing further growth."

Map Kowen Forest map

The naturally occurring fungi is recognised internationally as a significant threat to pine plantations, causing large scale dieback if trees are stressed or damaged by natural events like storms.

"In this particular case, there had been bad drought stress in the mid 2000s... and so dead tops were there already in some trees."

"We think that's been a factor in how aggressively the fungi has come in as a secondary agent after the hail."

Early harvest underway

Over 300 hectares of trees were damaged by the hail storm and then invaded by the lethal fungus, prompting the ACT Government to begin harvesting early.

"Even (though) many of the trees here that look as if they've died... many of those have got a little bit of green growth in them still, just clinging on, and the timber's sound," Mr Langdon said.

"We are racing against time a little bit though as we head towards warmer weather in the summer to harvest these (trees) before they start to decay."

Mr Langdon said the dieback was an extremely rare event for the ACT region, and a phenomenon he'd only witnessed once before in plantations at Tumbarumba.

But it's another major blow for ACT forests, which lost more than 10,000 hectares of pine plantation in the 2003 Canberra bushfires.

ACT Forests were substantially damaged by the bushfires of 2003. ( File photo: ABC News )

Kowen Forest plantation is one of the ACT's largest remaining viable timber plantations, and the ACT's insurers had already granted approval to begin harvesting and selling the timber.

While the trees are being harvested 14 years ahead of schedule, the timber won't be wasted.

The larger sawlogs are destined to be processed by Auswest Timbers in Fyshwick for building materials, while the smaller trees will be pulped for cardboard.

The government plans to replant pines in the area next winter, with the land eventually to be developed for housing in coming decades.

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