The Otago Daily Times understands the massive cocaine haul was stashed in an underwater panel on the hull of Spirit of Auckland, a vessel which docked in Philadelphia on August 2, then South Carolina on August 6.
The drugs were seized by US police that month.
According to online shipping records, Spirit of Auckland later visited Panama before stopping in Tauranga and Melbourne.
At 6.36am on Saturday it docked at Port Chalmers for a 16-hour stay.
It is understood the defendants had allegedly flown into the country and made their way to Dunedin, where they bought a significant amount of diving gear before heading to Careys Bay, just north of the port.
It is alleged one of the men used the equipment to search the ship for the consignment, unaware it had already been confiscated by authorities.
Ferreira-Sampaio and Hodder were remanded in custody by consent and may apply for bail when they return to court later this week.
The charge they face carries a maximum penalty of 14 years' imprisonment.
The investigation - dubbed Operation Por - illustrated the co-operation and strong partnerships police had with their international partners in targeting criminal activity, Detective Inspector Albie Alexander said.
Australian Federal Police refused to comment on its role in the investigation or whether it had the defendants under surveillance.
The United States Drug Enforcement Administration has been contacted for comment.
