Protected
The site is about 130km (80 miles) south of the Namibian harbour town Luderitz, in an area long sealed off for mining.
The mines are established by sea-walling the ocean and dredging the dry seabed for diamonds.
Portuguese gold coins are part of the recovered cargo
Pumps ensure the sea does not reclaim the land - an exercise that is costing thousands of dollars each week.
Bruno Werz, the archaeologist leading the excavations, said the shipwreck was particularly valuable because it had not been tampered with.
"This collection has not been disturbed by human interference," he said.
"We are very fortunate to have found an untouched wreck with all the material that was on site still here in one collection."
Archaeologists from South Africa, Namibia, Zimbabwe, the United States, the UK and Portugal are working on the excavation, which is due to be completed by mid-October.
Thereafter the detailed work of recording and preserving, which can take up to 30 years, can begin.
Stone and metal cannonballs and other artefacts are being covered with plastic and sand to protect them from sun and air.
Mr Ndoro said the shipwreck was a very important find for Africa.
"Here we have different African countries cooperating to make sure we have saved this ship and we have something we can show to the world."
"I am sure there will be many more wrecks to be found here," he added.
"Namibia should invest in training archaeologists."
