RNZN Naval Divers on the scene above HMNZS Manawanui, off the Southern Coast Of Upulo. Photo: New Zealand Defence Force
All three containers that came off the Manawanui have now been removed from the reef, according to the New Zealand Defence Force (NZDF).
Deputy Chief of Navy Andrew Brown describd the opertation as a "complex team effort" that took four days to pull off.
A statement from the NZDF said that two of the 10ft shipping containers were empty, while one contained food, which was buried at a landfill.
All three containers are being disposed off at the port.
Brent Ross, owner of surf tour business Offshore Adventures, previously told RNZ Pacific that food was spilling out from a container.
He said in one instance clients who were at a surf spot needed to get out of the water because the food had attracted sharks.
The Manawanui ran aground south of Upolu on 6 October.
The island nation is hosting the Commonwealth Heads of Government Meeting (CHOGM) this week.
Salvage and recovery operation efforts will be scaled down during the meeting.
However, Brown said monitoring will continue.
"This means one dive, one drone flight and one beach patrol daily, with the timing coordinated so as not to disrupt the event."
Meanwhile, Samoa's Marine Pollution Advisory Committee said a contractor would be selected to remove the remaining fuel from the vessel now that an insurance surveyor has completed their work.
The New Zealand Navy ship was carrying 950 tonnes - the equivalent of 950,000 litres - of fuel.
Committee chair Fui Tupai Mau Simanu said salvaging the fuel was expected to start in mid-November and take about 20 days, depending on the weather.
The committee reported up to 200,000 litres of diesel leaked from three places on the ship in the first week after it sank.