Six other children were among those who drowned. Turkey has stepped up efforts to stop migrants from leaving to Greece by sea.
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Several coast guard vessels, a Greek navy ship and a Super Puma helicopter are taking part in the rescue operation. In another incident six children drowned after a rubber dinghy carrying Afghan migrants to Greece sank off Turkey’s Aegean coast.
A wooden boat, thought to have set sail from the Didim district of Aydın province, capsized off the Greek island of Farmakonisi at around 4 a.m, Doğan News Agency reported.
“Greece can not become a warehouse of souls for people who don’t want to stay here”, Tsipras said.
More than 3,500 people have died or have been reported missing this year while trying to cross the Mediterranean into Europe.
Greece recently sought to return some 50 Pakistanis but Islamabad accepted only 20 of them, Prime Minister Alexis Tsipras said this week. Almost all have entered the country from Turkey, paying large fees to smuggling gangs who arrange crossings in small, overcrowded boats.
Germany announced this week that it has welcomed around 960,000 asylum seekers so far in 2015.
The latest drownings came as witnesses said Greek police started removing hundreds of refugees stranded on the Greek-Macedonian border and blocking rail traffic. The services are now expected to restart soon.
People considered “economic migrants”, from countries such as Morocco and Pakistan, have been stuck on the border for days or even weeks.
Police said 10 migrants were detained for resisting their transfer to the buses.
The humanitarian workers were asked to leave the area during the operation while journalists and photographs were told to keep the distance of about three kilometers “to protect them from any possible violence, tension or threatening and aggressive behavior”.
The bottleneck occurred after Macedonia blocked passage to those not fleeing war zones in Syria, Iraq or Afghanistan.
It says 911,487 refugees and migrants have reached the European Union since January, the vast majority crossing from Turkey to nearby Greek islands.
Local police officials said the migrants are taken on buses to Athens, where they will be accommodated in migration centers.
The coast guard said 26 people have been rescued alive.
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Five children, four men and two women died in the incident. Their nationalities were not immediately known.
