The women told journalists their boat was intercepted mid-sea by the Turkish coastguard, who began transferring migrants to their patrol vessel to return them to Turkey, starting with the children -- when the handler of their boat started the engine and sped off towards the Greek coast.
The two women of Kurdish origin, one of them pregnant, were picked up with the rest of the passengers by the Greek coastguard and taken to the island of Lesbos without their children, they said.
One of them, who gave her name as Deniz Sidur, said she had been travelling with her 20-year-old son Omar and another five children.
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The UN refugee agency's representative on Lesbos island, Boris Cheshirkov, said he had been informed "of an incident at sea that led to the separation of a family".
He added that a process had begun to bring the children back together with their mother.
"Contact has been established with their uncle, who remained with the children, and who says they were all taken to a road leading to a refugee camp in Turkey," Zoe Livaditis of the Red Cross told AFP.
The other woman was a mother of two children, whose age had not been specified. Authorities are currently verifying her testimony, in order to launch a reunion procedure should her claim be proven.
According to EU police agency Europol, over 10,000 unaccompanied migrant minors have disappeared in Europe since January 2014 following their arrival.