The Ports of Auckland is moving all commercial vessels back to the Waitemata seaport as the tsunami alert is downgraded to an advisory.
Ships were moved out before 10am on Sunday, including the Dawn Princess cruise ship.
The ports company says all vessels will remain on standby to leave the port at short notice during the next 12 hours.
It says it is continuing to take a cautious approach and the decision to resume operations was made in conjunction with other local authorities.
The tsunami alert prompted the Port of Napier to close at 3am on Sunday.
The duty pilot said all ships in port were escorted out into water of at least 30 metres deep in Hawke's Bay.
Other vessels, which were due in port on Sunday morning, waited off the coast of Napier.
A visit by a cruise ship was cancelled. It is now going directly from Wellington to Tauranga.
Meanwhile, water receded at Waikanae beach near Gisborne.
The Emergency Management Office there confirms the water has been receding.
Controller Jon Davies says there was a sudden drop of up to a metre in places.
Civil Defence in the Hastings district later advised residents from the coastal settlements of Te Awanga, Haumoana, Clifton and Whirinaki, that they could return home.
A welfare centre was set up at the Haumoana School at about 9am and 200 people turned up for cups of tea and coffee.
Following a re-assessment of the situation, Civil Defence Controller David Fraser said people could return home, but should still stay away from the beach.
Tsunami surges in Tutukaka harbour
In Northland's Tutukaka Harbour boats headed out to sea to avoid the surges, that had damaged the marina in the last tsunami.
A tourist operator Jeroen Jongyens says some boats crashed into each other in a last-minute rush to get out.
There were also delays to the Interislander ferries due to the temporary closure of Tory Channel in the Marlborough Sounds.
Tide levels receded 30 - 40 metres at Lyall Bay on the south coast, before flowing back in. Resident Richard Kenan says there were no real dramas.
The Wellington dragonboat festival in Wellington harbour was cancelled.
A number of events on the coast around Auckland have been cancelled - including the Cathay Pacific half marathon, beach races at Onetangi and the Kaiaua Wine & Food Festival.
However, some surfers at west coast beaches in Auckland ignored the tsunami warnings.
Waitakere Mayor Bob Harvey said the Piha surf lifesaving club was forced to open a very small section of the beach because of determined swimmers.
Mr Harvey said he is not happy about the situation, and it has been incredibly difficult for civil defence personnel to keep swimmers and boaties out of the water.