Waka Kotahi contractors have been using builder's foam to fill in potential bat roosts on the route of the proposed Mt Messenger bypass in Taranaki.
The revelation comes a month after the Waka Kotahi - the New Zealand Transport Agency - said no roosts or potential roosts of the endangered long-tail bat would be disturbed before the project on State Highway 3 officially got the green light.
The bypass will run from Uruti to Ahititi, a stretch of about 6km that will avoid the existing steep, narrow and winding route over Mt Messenger on State Highway 3 north of New Plymouth.
As well as safety improvements it will save motorists between four and six minutes driving time.
A memo released under the Official Information Act summarised ecological activities undertaken along the proposed route under the auspices of the Wildlife Act during April.
It said bats were observed but concluded no roosts were present on the route due to a lack of swarming activity indicative of roosting, and contractors then set about destroying potential roost sites.
On dozens of trees identified as suitable for bat roosts they removed epiphytes and flaking bark, and filled in cracks and crevices with natural material or with builder's foam.
That was despite Waka Kotahi saying in August that its inspection teams had not discovered any bats or disturbed any areas suitable for bat roosts.
The Poutama Charitable Trust opposed the bypass and spokesperson Marie Gibbs said it was disappointing Waka Kotahi seemed to be saying one thing and doing another.
"More importantly than that it's concerning that they've actually done what they've done and gone into the ngahere and blocked up those bat holes right before winter," Gibbs said.
"And we see that as totally unnecessary particularly if this proposed project doesn't eventuate."
Waka Kotahi appeared to be a law unto itself, Gibbs said.
"It's been an eye-opener for me how often this type of behaviour goes on. It's not something you would expect from a government agency like NZTA.
"It seem to me that what we are seeing a lot with the Mt Messenger project is that these government departments seem to think they are above the law."
Gibbs was also concerned about how much the Department of Conservation knew about the activity.
Whenua Warriors - a conservation group - presented an online petition with about 20,000 signatures to Transport Minister Michael Wood. It called for the $280 million project to be scrapped.
Whenua Warriors member Emily Bailey said Waka Kotahi's mixed messages did not fill her with confidence.
"It's pretty frustrating because up until last week they were still saying they might do it [block off bat roosts] in the future and then this memo says they've actually done it months ago, so how are we meant to believe anything they are saying if they talk like that."
Bailey was also not convinced by the argument that the disturbing of potential bat roosting sites was necessary to protect the native mammals in the long term.
"Basically what they're doing is destroying habitat that bats could use so they can get their road through because there aren't any bats in the way, but if they just left it maybe the bats would be there and the road couldn't be built."
Instead of building a bypass they should upgrade the existing road, she said.
Waka Kotahi's director regional relationships, Linda Stewart, acknowledged the wording of its previous statements about the bats could have been worded better.
"Specifically, where we have previously said: 'We will not take any action to prevent bats from roosting in trees until the project begins in earnest', it would have been better to say: 'No action will be taken to prevent bats using existing roost sites'."
She regretted any confusion the agency had caused.
"We want to ensure the risk of felling a tree with a bat roosting in it is reduced to an absolute minimum and are committed to ensuring bats are fully protected both before and during construction."
The work was reversible if the road did not get resource consents, she said.
Meanwhile, the Department of Conservation (DOC) confirmed it knew about the work.
Its statutory manager for the Hauraki-Waikato-Taranaki region, Michelle Lewis, said DOC did not have any legal mechanism available to it under the Wildlife Act to permit or refuse what Waka Kotahi was doing in relation to bats at Mt Messenger.
But she said DOC was comfortable with measures the transport agency was taking to avoid disturbing bats.
Pending court appeals, construction is earmarked to begin at Mt Messenger in September next year.