I am inclined to believe the French version of this story.
The Greek vessel spotted a Tanzanian-flagged cargo ship, Cirkin, a squat white-and-blue boat, suspected of being used by Turkey — a NATO ally and still officially an EU membership candidate — to transport tanks and weapons to Libya's U.N.-recognized government. The Spetsai dispatched its helicopter, a Sikorsky S-70B Aegean Hawk, to take a closer look. But the helicopter and the Spetsai were tersely warned off by three Turkish naval ships, which said the cargo boat was carrying medical supplies, and under their protection. On orders from an Italian commander, the EU forces backed away and reported the incident to EU and U.N authorities.
If it wasn't carrying arms, why were the Turks all in an uproar (beyond the usual "you are Greek, therefore we don't like you" business).
... the same small Turkish flotilla encountered a French frigate, the Courbet, that is part of NATO's Operation Sea Guardian. At that point, the French said, the Cirkin's Automatic Identification System was off.
According to the French defense ministry, which lodged an official complaint, the Turkish ships became hostile when the Courbet, acting on the orders of NATO's Allied Maritime Command, headquartered in the U.K., sought to inquire about the Cirkin's destination and payload.
And the 'escorts' objected, doubtless on orders from Ankara.
What seems clear is that Turkey did not want its own allies to see whatever the Cirkin was carrying. And its cargo was delivered without being inspected, despite orders from commanders leading the different EU and NATO maritime missions.
I love this politico double talk, though.
"Turkey is a valid ally," Portuguese Defense Minister Joćo Gomes Cravinho said in an interview. "I wouldn't call it a problem, but there are a number of problems relating to Turkey."
The French minister's observation that NATO was experiencing 'brain death' is also amusing.