The Mexican government has said it would continue to receive cruise ships "for humanitarian reasons", but that passengers would be "individually fumigated" before being taken to airports for return flights to their home countries.
The Transportation Department said in a statement on Wednesday that protocol had been applied to the MS Europa, which docked in the Pacific coast port of Puerto Vallarta and was cleared of passengers over the weekend.
The department said Mexico's position is that "cruise ships can disembark for strictly humanitarian reasons, without endangering the port's population".
Such passengers would be transported directly to the airport and not wait in lines or go through check-in at the gates, but would instead directly board planes.
It is unclear whether there are any more stranded passengers aboard cruise ships in Mexican waters.