But it vowed that the massive port, gateway to the Aegean islands for hundreds of thousands of holidaymakers every summer, will be emptied "in a few days."
"Do not lose your courage, we stand by you, we love you...!" reads a leaflet that will be distributed at the port from Monday, the merchant marine ministry said.
The leaflet in Arabic, Farsi, Greek and English urges migrants not to trust smugglers and to refrain from violence in the wake of several brawls between rival nationalities at the port in past weeks.
Although Greek authorities have so far pledged not to use force against the migrants, the document says that "in a few days the port of Piraeus will be emptied (evacuated)."
The authorities offer few guarantees as to the migrants' future beyond the provision of accommodation and healthcare at organised migrant facilities.
"Since other European states have closed their (borders) it is true that nobody can be sure for the exact course of events to come," the leaflet says.
Greece is running out of time to clear the port before the celebration of Orthodox Easter on May 1, a period of busy traffic to the islands through Piraeus.
"From now on, the port of Piraeus will have to service significant volumes of traffic of vehicles and passengers," it adds.
According to the government, there are still over 4,600 people in the makeshift camp of Piraeus that has taken over a number of passenger terminals.
Overall, there are over 52,000 people trapped in Greece after Balkan states further north closed their borders to migrants.
Efforts to persuade the migrants to relocate from Piraeus to other camps have so far met with only limited success, as only a few hundred people have left, fearing that they will be trapped inside closed camps under police guard.
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