The 320km stretch of sea between Libya and the islands of Crete and Gavdos, has become a popular route for asylum seekers heading to Greece.
Greek authorities say one person is dead and 25 are missing after a boat carrying migrants sank off the coast of Gavdos island near Crete on Sunday.
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The Greek coast guard said they rescued 51 people from the water.
A search and rescue operation was launched under the coordination of the Joint Search and Rescue Coordination Centre (JRCC), in the sea area 38 nautical miles south of the island of Gavdos, after the alarm was raised about a boat carrying migrants.
The search mission involved patrol boats, a helicopter and a drone as well as commercial vessels were involved in the search assisted by the European Union border protection agency, Frontex.
High winds were reportedly making the search effort more difficult.
The 320km stretch of sea between Libya and the islands of Crete and Gavdos, has become a popular route for asylum seekers heading to Greece.
The search is expected to continue through Monday, with authorities trying to locate any survivors or evidence that could lead to the discovery of the missing people, across a large sea area south of Gavdos.
Frontex has reported at 25% drop in migrant crossings in the Eastern Mediterranean in the first eight months of this year, compared to last.