GNS Science says it was taken by surprise by the tsunami that followed last Monday's earthquake.
The Crown research institute said it was not the only one - its international colleagues were also caught out.
GNS director Ken Gledhill said it was clear from satellite radar and GPS that the earthquake ruptured several faultlines from Culverden to Cape Campbell.
But one of them behaved in an unexpected way.
"The tsunami turned out to be a surprise, and it wasn't a surprise just for us - my international colleagues had the same issue," Dr Gledhill said.
"Large on-land earthquakes do not usually cause tsunami - we did not know it had gone off-shore."
At the same briefing this afternoon, Civil Defence director Sarah Stuart-Black said people should not rely on official tsunami warnings alone.
"People should heed those natural warnings. If it's so strong that people have trouble standing up; or is rolling for more than a minute; or the sea comes up higher or it recedes out, people should immediately evacuate inland or uphill and that is critical."
No system could provide that assurance when communities had less than minutes to make a decision, Ms Stuart-Black said.
NZ First wants inquiry
New Zealand First is calling for a public inquiry into the state of the country's resilience to major natural disaster.
Its leader, Winston Peters, said some of the response to the earthquake was inadequate, such as the tsunami warning and the 111 system.
It appeared the nation did not learn anything from the Canterbury earthquakes, he said.