Transport officials have been given permission to kill seals along the damaged Kaikōura coastline but have promised not to do so.
The Transport Agency today obtained a Department of Conservation permit to cull seals after State Highway 1 north of the town was damaged during the 7.8 magnitude earthquake last November.
The earthquake also triggered a large slip at the Ohau Point seal sanctuary and, despite fears the population was wiped out, some seals survived and relocated.
The permit was applied for last year, and gives the agency and KiwiRail permission to herd, injure and kill seals disrupting construction work while SH1 is being repaired.
It was required as the animals cannot usually be touched, under the Marine Mammals Act.
Agency recovery manager Steve Mutton said the permit gave some people the wrong idea, and there were procedures to ensure no seals were deliberately killed.
"The Transport Agency and KiwiRail would never kill a seal to reinstate the road and rail - this measure's in place to enable us to go in and move the seals out of harm's way," he said.
Seals might be killed unintentionally, but the agency had steps in place to protect wildlife.
"That's everything from herding the seals away from the construction zone ... We're trialling fences, putting them up, to ensure the seals don't come back to where we're working," he said.
Mr Mutton said they were also using helicopters every morning to fly low over the rocks and herd the seals away.
Department of Conservation director-general Lou Sanson said during the rebuild the seals could become accidental collateral damage.
"So we're talking masses of explosives, we're talking of seals coming in at this time of year, so we're allowing them to move the seals.
"We know there have been accidental deaths so we're basically just saying we're not going to prosecute them."
'Harsh' permit language a legal requirement - DOC
The department's South Island operations director, Roy Groves, said the harsh language in the permit was required by law.
"While the wording of the permit sounds quite harsh, the majority of the work they will be carrying out under that permit is herding seals away from big machinery," he said.
Mr Groves said the decision to hand out a permit like this was not done lightly.
"These are exceptional situations ... they are not something we hand out to everyone," he said.
Kaikōura mayor Winston Gray said it was easy to misconstrue the facts and some media reports were completely wrong.
"I was very disappointed to read it [reported incorrectly] ... it was sensationalism and it read like it was open season on seals," he said.
Mr Gray said the permit allowed workers to get the job done without fear of legal action.
The permit lasts until next March.