KiwiRail says a shipment of imported hardwood sleepers has tested positive for two types of fungus that are not found in New Zealand.
In July, the state-owned rail operator admitted that 7000 of the 100,000 sleepers imported from Peru were rotting and said it hoped to replace them by next year.
Initial tests on the decaying sleepers revealed a fungus common to New Zealand.
However, further DNA tests done only on a new shipment still in a workshop have shown up two new types of fungus.
KiwiRail says the Ministry for Primary Industries has been alerted and will investigate whether the fungi pose a risk to biosecurity.
At the ministry's instruction, KiwiRail is using a household bleach on the rotting sleepers as it removes them.
Mr Quinn says KiwiRail is doing all it can to mitigate any risk by applying the bleach and covering the sleepers.
"Out of the work that we do over the coming weeks and months we will find out what the best way to dispose of it is."
New Zealand First wants someone to be fired after KiwiRail admitted railway sleepers are harbouring a foreign fungus.
New Zealand First transport spokesperson Brendan Horan says the fungi could inflict dramatic damage on the environment.
Mr Horan says many bridges are affected which could mean the fungi enters waterways.