The captain of a freighter which was shot at has condemned the act as “disproportionate”, and showing no regard for human life.
The ship was sailing from the city of Iskenderun, near the Syrian border, and headed to another Turkish port when they were fired upon, according to the foreign ministry in Turkey.
Sami Kalkavan, captain of the M/V AC, said the Greek coastguard had ordered the vessel to dock for inspection at Rhodes, some 15 miles from the Turkish coast.
When they failed to reply, the coastguard put 16 bullet holes in the ship.
Mr Kalkavan, said: “The coastguard asked for the ship to be docked at the port at Rhodes immediately, and we did not accept this.
“They wanted to check the ship, and we didn’t accept that.
“They said they would fire if we didn’t stop – they did what they said.”
After the altercation the freighter moved back into Turkish waters.
But the incident has angered Ankara, with the foreign ministry issuing a statement, saying: “There is no justification for firing on an unarmed commercial ship carrying freight between two Turkish ports.
“Our sole consolation is that nobody was killed or injured as a result of the incident.”
The Greek coastguard claimed it fired warning shots as it attempted to inspect the cargo after receiving an anonymous tip-off it was carrying contraband.
Two Turkish coastguard ships were also said to be at the scene.
Historically the two countries have a tense relationship, with territorial disputes nearly leading to a war in 1996.
Last year, after Turkey’s failed coup, Athens angered Ankara when it failed to hand over Turkish soldiers who had fled to the neighbouring country amid suspicions they were involved in the putsch.