All three containers that came off the Manawanui have now been removed from the reef.
The ship sank last month after running aground off the south coast of Upolu in Samoa.
Locals previously reported food was spilling from one of the containers.
Deputy chief of Navy Andrew Brown said removing the containers was complex and it took four days to do.
The navy will continue monitoring Manwanui during the Commonwealth Heads of Government Meeting which is currently being held in Samoa, with one daily dive, drone flight and beach patrol, he said.