They estimate the drugs have a street value of more than $1 billion.
Federal prosecutors call it one of the largest cocaine seizures in USA history.
The cocaine bails were transported by boats to the container ship while it was at sea, authorities said.
At least two crew members of the Gayane have been charged with trafficking, according to a complaint filed Tuesday by the U.S. Attorney's Office.
Instead, US authorities seized the haul, totalling about 14.5 tonnes with an estimated street value of US$1 billion (AUD$1.4 billion), according to federal prosecutors.
The U.S. Attorney's Office, Customs and Border Protection and Philadelphia Police did not immediately return requests for comment Tuesday.More news: Scary news for 1.4 billion Apple iOS users!
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MSC ships were recently the subject of a bust in Philadelphia.
Last March, federal agents seized 3,200 pounds of cocaine concealed behind crates of fruit on a ship at the Port of NY and New Jersey. Check out the tweets from the US attorney below.
"This is one of the largest drug seizures in United States history", U.S. Attorney for the Eastern District of Pennsylvania William McSwain tweeted. The Inquirer also reports that the bust happened after a member the Coast Guard found traces of cocaine on Durasevic's arms. It wasn't immediately clear the number of crew members who have been arrested.
Online ship trackers said the vessel detained in Philadelphia sails under the flag of Liberia and arrived in Philadelphia after 5 a.m. Monday.
The ship's previous ports of call were the Bahamas on June 13, Panama on June 9, Peru on May 24 and Colombia on May 19, records show.
"MSC takes this matter very seriously and is grateful to the authorities for identifying any suspected abuse of its services".