The embarrassing disaster is NZ's first naval loss during peacetime, and first since World War II.
It has also started the clock on an urgent clean-up job, and investigation into whether the wreckage can be salvaged from the sea floor.
On Saturday night, the 85m vessel ran aground around 2km south of the Samoan village of Siumu, causing Captain Yvonne Gray to order crew to abandon ship via life rafts and smaller vessels.
All 75 on board - including seven scientists and four non-NZ military personnel - made it to shore in rough seas, which took at least five hours during the night.
One life raft capsized on the reef, requiring those on board to walk to shore on the reef, where several required medical treatment.
On Sunday morning, the listing boat caught fire and sunk.
Defence Minister Judith Collins said her top priority, given all crew were safely transported from the sinking vessel early on Sunday, was "the environmental side".
"It's got a lot of oil on board. It's got all sorts of things. It's got lubricating oil, hydraulic oil, diesel ... it's got a lot of stuff in it," she told Newstalk ZB.
"I don't think we can leave it like that."
My thoughts this morning are with the officers, crew, and passengers on the HMNZS Manawanui. Many thanks to the Samoan people for their brave assistance.— Judith Collins (@JudithCollinsMP) Our families will be shocked at what happened, but grateful for the successful rescue.I will be joined by Chief of Navy for a…October 5, 2024
Samoan man Manu Percival, interviewed by Radio NZ on Monday morning, said oil was identifiable along the coast for several kilometers which would have a "massive impact".
"The impact is crazy. There's so many green sea turtles in that area. So many sting rays," he said.
"Right where the ship went down just inland, there's a huge lagoon of brackish water and it houses all sort of animals. Coconut crabs, everything. They'll all be affected. Everything.
"That part of the ocean is full of the grass that turtles eat. That's going to have oil all over it for sure."
Mr Percival said the sea was "big time" treacherous and locals avoided it.
The Manawanui, a specialist hydrographic vessel, was in the region to map the ocean floor in the area for the first time in almost 40 years.
"They were dealing with a reef that has changed ... there have been earthquakes, there's been tsunamis, there's been changes to that reef and that's why that survey was taking place," Ms Collins said.
She said the court of inquiry, which will take up to two months, would explain how the ship lost power and ended up on the reef.
Whether the wreckage will be salvaged will depend on how deep it is below the surface, which was being investigated.
Acting Samoan Prime Minister Afioga Tuala Tevaga Iosefo Ponifasio told a press conference he believed it was "not recoverable".
The lost ship is the latest setback for New Zealand's defence force, which has been hit by attrition - like many countries - and belt-tightening in recent years.
Former defence minister Andrew Little described the pandemic-era staff loss as "a big hollowing out", with 2023 headcount equivalent to 2015 levels.
In 2023, four of the navy's nine vessels were unable to be staffed, which Ms Collins told AAP was a "real concern".
It is not clear whether under-staffing or other budget cuts had an impact on the ship running aground, which will be the subject of the defence probe.
The ship began life as a Norwegian-built oil tender in 2003 before being purchased in 2018 for $NZ103 million ($A93 million) and entered service in 2019.
Defence chiefs opted for the second-hand vessel - which was expected to last through to the mid-2030s - rather than a new build due to budgetary constraints.
11°C