HMNZS Canterbury - the first and biggest of the Navy's Protector fleet vessels - sailed into Auckland yesterday minus one of its inflatable boats.
Commanding officer Commander Tony Millar said a rogue wave took out one of two 8m rigid hull inflatable boats in Tuesday's storm.
He said conditions were among the "10 worst" he had sailed in.
But the 131m, 9000 tonne ship performed well, he said.
The ship will be based at Devonport Naval Base for at least the next month while its capabilities are tested and its crew fully trained. Trials would be carried out with the Army and Air Force because the vessel could carry up to 250 soldiers and helicopters could land on board.
"Because she's a new ship, it's a matter of getting used to how she operates," said a Navy spokeswoman.
The vessel was said to embody the the Defence Force's joint approach to operations.
HMNZS Canterbury, built in Holland and commissioned in Melbourne in June, left Timaru on Sunday before stopping in Wellington on Monday. Open days and a series of visits around the country later this year are planned.