The Japanese tsunami reached every coast, beach and inlet in New Zealand, in places doubling the height of waves.
New data released by Niwa showed that sea levels peaked in Whitianga and the Chatham Islands, where the tide was lifted 80cm, producing 1.6-metre waves.
Mt Maunganui and Timaru also recorded waves greater than 1m.
The tsunami, which initially travelled at 800km/h, even touched Scott Base in Antarctica, where sea levels were lifted 10cm.
Niwa principal scientist Rob Bell said that the first waves arrived 12 hours after Friday's quake, but the largest swells hit the coast much later.
In Timaru and Sumner, the largest wave height did not occur until 33 to 40 hours after the first wave hit.
"It's not safe to assume that once you have seen one wave, the risk subsides and all returns quickly to normal.
We are recording obvious wave heights now, days after the earthquake, which are affecting currents in harbours and estuaries," said Dr Bell.
The delayed waves were due to the tsunami bouncing off continental shelves all around the Pacific, including South America and local offshore ridges.
Dr Bell said: "The tsunami fights its way through all the land masses, so the west coast would've received waves through the Solomon Islands.
"On the east coast, it came around Samoa and over the Kermadec trench. So you get a double tongue that goes down both coasts."
The worst damage from the tsunami in New Zealand was reported in Marlborough, where strong currents tore through mussel farms, at a cost of several hundred thousand dollars.
The greatest "far-field" tsunami threat to New Zealand is from South America. Fault movement in Chile in 1868 generated the largest known tsunami on New Zealand shores - 8m high in parts of the east coast.
There is also a local tsunami risk to Gisborne, Hawkes Bay and Bay of Plenty coastal areas due to potential fault movement and underwater landslides on the Pacific Ring of Fire.