Greece accused Turkey on Friday of trying to provoke it by trying to push boats carrying migrants into Greek waters.
Turkey and Greece disagree on a range of issues, including energy resources in the Mediterranean, and tensions between the NATO allies rose last year when thousands of asylum-seekers tried to invade the Greek border in Turkey.
Notis Mitarachi said the Turkish coastguard and its navy had reported multiple incidents on Friday of the Greek coastguard and migrant boats to Europe border in an attempt to provoke an escalation with Greece.
It is beyond doubt that these migrants departed Turkish shores and were not at risk by Turkey, Mitarachi said in a recorded statement.
We call on Turkey to stop this unwarranted provocation and to stand down.
The Turkish Foreign Ministry said it was not aware of the incident while the defence ministry did not immediately respond to a request for comment.
Greece has also accused Turkey of harassing its vessels in the eastern Mediterranean and taking provocative actions.
The Turkish coastguard said that in one incident a boat carrying migrants tried on Friday to enter Greek territorial waters accompanied by a Greek coastguard vessel. In another, two Greek vessels tried to push a dingy with migrants into Turkish waters.
In a third incident off the island of Lesbos, a Greek coastguard vessel entered Turkish territorial waters and attacked a Greek patrol boat, it said.
Nearly a million asylum-seekers, mostly Turkey, crossed from Turkey on boats to Greece in 2015 at the beginning of the migration crisis in Syria. A year later, the EU struck a deal with Ankara to reduce the flow of refugees and the number was dramatically reduced.
Mitarachi called on Turkey to live up to its commitments under the deal.