Local people had gone out in small boats to the floating containers, taking consumer goods including bicycles and clothing.
Port officials said 45 containers had worked loose from the ship’s deck.
An investigation is under way to work out the cause of the accident.
They said they had chased down two speed boats loaded with goods.
Local media said the Brazilian-registered ship, the Log-In Pantanal, unloaded 248 containers at the Port of Santos on Thursday and took 341 on board.
The company responsible for the ship said it believed the accident had been caused by bad weather.
Social media videos showed the ship rolling heavily in a high sea swell.
Eyewitnesses told reporters that some of the containers had burst open on impact with the water.
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