Five boats sailing nearby, two patrol boats, a Coast Guard plane and helicopter were searching the area southwest of the Peloponnese, the ministry added.
The Piri Reis, carrying a crew of 17 Syrians and flying the Cook Islands flag, sank before 0600 am (0300 GMT) after colliding with another cargo ship, the Consouth, as it was transporting fertiliser from Algeria to Ukraine, it said.
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The Consouth, flying the Antigua-Barbuda flag, plucked seven crew members from the sea after they managed to escape the wreck.
It was sailing empty towards Malta with a crew of 16 sailors, the ministry said.
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