West Coast Civil Defence regional manager Chris Raine has said sorry for issuing the advisory.

"I apologise. It was done in the best interests of the West Coast people," he told Fairfax. "I withdraw the urgent warning completely."

National Civil Defence, which operates separate to regional bodies, says it had been given no indication West Coast Civil Defence was going to issue the warning.

On its Facebook page, it said media ran the warning in good faith.

"The science we have from GeoNet is the same as we had on Monday - it's just their [West Coast Civil Defence] interpretation," a national Civil Defence spokesperson told Newshub.

Another spokesperson said they had been in contact with West Coast Civil Defence, and expressed disappointment that "there were inaccuracies in the release".

In the since retracted warning, West Coast Civil Defence Public Information Manager Andy Thompson said the aftershock activity in the area been "suspiciously quiet".

"The GeoNet seismograph drums have been very quiet for the last day or so and the normally higher aftershock sequence of large quakes has not been occurring in the Kaikoura area."

Mr Raine said in the warning another worry is that an area in Arthur's Pass slightly west of the divide has experienced a number of small tremors in the last few days.

He said it's an area they have been monitoring closely, with Mr Thompson describing it as "highly sensitive".

But GeoNet say the science they're using to authenticate the warning is simply incorrect.

"Just because the drums have been quiet for a day means absolutely nothing," GeoNet seismologist John Ristau said.

"We kind of want to distance ourselves from this - we don't know why they've gone out and done this."

Mr Ristau says it is not usually Civil Defence's policy to issue a warning without checking in with them first.

"Civil Defence would talk to us, we advise them, and they would never release anything without talking to us.

"What [West Coast Civil Defence] has done is look at our [seismograph] drums, and taken the information we've put out and made their own interpretations."

The Ministry of Civil Defence spokesperson reiterated that it is in regular contact with GeoNet, and would seldom issue a warning without consulting it first.

Last week, GeoNet warned residents in Wellington and the top of the South Island there's a 93 percent chance of an aftershock between magnitude 6 and 6.9 in the next month.