Federal authorities arrested and charged two of the ship's crewmembers Ivan Durasevic and Fonofaavae Tiasaga.
The drugs were transferred in containers aboard the ship.
Several crew members allegedly helped transfer bales of cocaine.
Fourteen boats approached the ship during its most recent journey and the crew members are accused of helping to move the drugs from those boats.
An online court docket does not list defense attorneys for the defendants. It is unclear whether there are other such containers.
According to a senior Justice Department official, U.S. Customs and Border executed the seizure based on a joint investigation between the Department of Homeland Security and Drug Enforcement Administration.
More than $1 billion worth of cocaine was seized by federal authorities at a Philadelphia port Tuesday.
In this representational image, bags containing drugs are pictured as the Peruvian Interior Ministry burns more than seven tons of seized drugs, mostly cocaine, at a police facility in Ate, on the outskirts of Lima, Oct. 11, 2016.
The bust comes after USA authorities seized almost 1.5 tonnes of cocaine in March - the biggest haul in almost 25 years at the port of New York/Newark.
Meanwhile, reports said that this drug haul is the latest along the East Coast. According to VesselFinder.com, in the past month, the ship has docked in Freeport, Bahamas; Cristobal, Panama; Callao, Peru; and Buenoventura, Colomia.
Federal agents raided the MSC Gayane on Tuesday and seized the cocaine from the Swiss-owned company's ship. According to Philadelphia police, that is one of the biggest drugs seizures in U.S. history.
The shipping company MSC has been made aware of the find, saying "it takes this matter very seriously" and looks forward to cooperating with the United States authorities.
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