The drugs were valued at $1.3 billion.
U.S. Attorney William McSwain says Customs and Border Protection officials obtained a warrant Thursday and seized the MSC Gayane.
The cargo ship is owned by Swiss firm MSC Mediterranean Shipping Co.
McSwain says the ship is subject to possible forfeiture to the U.S. The value of the ship and its other contents hasn't been released.
MSC is one of the world's largest shipping lines in terms of containers. An email seeking comment on the ship's seizure wasn't returned Monday.
At least six crew members have been charged with conspiracy to possess cocaine aboard a ship. The federal investigation continues.