Kauri dieback has already been detected in Northland, the Waitakere Ranges and on Great Barrier Island.
Tracks have been closed in affected areas because the spores can be picked up on trampers' footwear and spread to other areas.
Kauri dieback disease is caused by a microscopic, fungus-like organism which infects the trees' roots and damages the tissues that carry nutrients and water within the tree, effectively starving the tree to death. Nearly all infected trees die.
"Dieback has spread though the North Island forests and represents the single biggest threat the species has ever faced," Ms Barry said.
Government committed $21.6 million to fighting dieback last year, half of which would go towards improvements to walking tracks.
Ms Barry today confirmed the start of the track upgrade programme.
Around 100km of paths will be upgraded to remove mud, which can carry the disease.
And 5km of boardwalks will be installed to keep walkers' feet clear of tree roots.
Up to 300 cleaning stations will be set up at track entrances and exits.
Further investment is going into researching the disease, which currently has no cure.