Oceanex said a windy blast blew the empty container into the harbour.
The container drifted across the water before it had to be towed to safety. A small boat nudged the container to a harbour wall where a tugboat came to its rescue.
There were no injuries or collisions.
Photos of the strange sight appeared on social media, including Twitter.
Environment Canada issued a wind warning for parts of Newfoundland today, including St. John's, with gusts of about 100 km/h.