President Recep Tayyip Erdogan has ordered the Turkish coastguard to prevent migrants crossing the Aegean sea because of the risks, officials said.
"On the orders of the president... permission will not be given for migrants to cross the Aegean sea because it is dangerous," the coastguard tweeted on Friday.
"The approach of not intervening against migrants wishing to leave Turkey remains in practice but this (new) approach covers sea crossings because of the dangers," it added in another tweet.
The coastguard said 97 migrants were rescued on Thursday after "the Greek side flattened three boats and left them in a half-sinking state in the middle of the sea".
The instruction comes after Erdogan said last week that refugees and migrants would not be prevented by Turkish authorities from leaving Turkey if that was their wish.
Thousands of refugees and migrants have also gone to the land border between Turkey and Greece where clashes erupted again on Saturday between Greek police and migrants.
During a tense stand-off, Greek police fired tear gas at migrants who responded to the officers by throwing stones and shouted "open the gates", according to AFP journalists at the scene.
The Greek police also used water cannon to stop the migrants, a correspondent said, many of whom have been stranded for days at the Pazarkule border, known as Kastanies on the Greek side.