Five other migrants were rescued, the officials said, and coast guard vessels assisted by a helicopter were searching for more survivors.
The incident occurred a day after two ferries took more than 120 migrants back to Turkey from the Greek island of Lesbos, in the second round of returns under an EU deal with Ankara to halt mass migration across the Aegean Sea to Europe, Reuters reported.
The accord, which came into force on Monday, aims to stem an uncontrolled influx into the European Union of people fleeing war and poverty in the Middle East and beyond, after more than 1 million arrived last year.
The United Nations refugee agency (UNHCR) and human rights groups say the accord may violate international law.
Although flows have slowed, migrants continue to reach the Greek islands. Greek authorities said 149 had arrived on Lesbos, Samos and Chios in the 24 hours to Friday morning.