Workers will not be in trouble if they move or accidentally kill seals while rebuilding earthquake-damaged State Highway 1 around Kaikoura.

A Department of Conservation permit gives NZ Transport Agency and KiwiRail staff permission to move the large number of seals around Ohau Pt without fear of prosecution under the Marine Mammals Act.

"It is a legal requirement to obtain these permits in order to move or herd seals, and carry out the restoration work on the road and rail corridor without the risk of workers being prosecuted in the event of any accidental harm," says DoC operations director for northern South Island Roy Grose.

"These permits have been issued in exceptional circumstances to allow vital work following a significant seismic event."

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Thirty-four seals reportedly died in March at two slips near the most unstable part of the northern side of Ohau Pt but Grose said it has not been possible to separate natural deaths - such as by natural rock falls - and the road reinstatement work.

The permit covers workers repairing the highway between Ohau and the Clarence River until March 2018.

Grose said the summer pupping period is over, but it is not clear what the long-term impacts on seals in the area will be.

- AAP