The Eleftherios Venizelos left the island of Kos with some 1,700 Syrian refugees on board and was expected to arrive in the northern port city of Thessaloniki tomorrow morning, after calling at the islands of Kalymnos, Leros and Lesbos to pick up another 900 people.
The Syrians will be put on buses to the border with Macedonia, officials said.
"The situation is out of control," Leros mayor Michalis Kolias said in a letter to the government, asking for help in getting hundreds of migrants off the island.
A record 107,500 migrants arrived at the European Union's borders last month, according to new figures released by border agency Frontex, a dramatic increase that is creating a humanitarian crisis for the 28-nation bloc.
Greece has seen around 160,000 migrants - virtually all of them fleeing war and persecution in Syria, Afghanistan and Iraq - land on its shores since January, according to the UN refugee agency.
The Greek Aegean islands close to Turkey have borne the brunt of the influx, with authorities overwhelmed and rights groups criticising miserable conditions facing the migrants, who are often forced to sleep in the open for weeks and queue for days to secure departure papers.
"There are no ferries available at present (and) next week there will be a problem as the ferries will be at near 100 percent capacity," association chairman Michalis Sakellis told Vima radio.
Greece is giving Syrian refugees priority in registration and embarkation for the mainland, over other nationalities such as Afghans and Pakistanis.
On Lesbos, scuffles have routinely broken out between non-Syrian migrants stuck on the island, and an aid group yesterday warned the situation was reaching "breaking point".
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