The Greek coast guard says four operations began late on Friday and one was still under way.
Three operations, including the ongoing one, involved separate incidents off the island of Gavdos, south of Crete, and the fourth took place off the southern Peloponnese region on the southern mainland.
In the ongoing operation, 39 people were rescued and taken to Crete, the coast guard said.
Five bodies were retrieved from the water. Survivors have said that dozens of others were in the same boat.
A total of nine vessels, including coast guard ships, an Italian navy frigate and four merchant ships, were still involved in the rescue Saturday, as well as two helicopters, the coast guard said.
In the other two operations off Gavdos, 47 and 89 people, respectively, were rescued.
Another 28 migrants were rescued off the Peloponnese, with no one reported missing.
The coast guard conducted extensive overnight search and rescue missions assisted by navy helicopters and commercial vessels as well as vessels from the European border protection agency Frontex.
Greek government officials say the spike in migrant arrivals is being driven by conflicts in the Middle East.
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