Turkey accused the German navy on Monday of conducting an "unauthorised" search on a Turkish-flagged cargo vessel in a bid to enforce a United Nations arms embargo on Libya.
But the European Union's Operation Irini - tasked with halting arms shipments to the strife-torn north African country - said it had made a "good faith" effort to get Turkey's consent for the inspection and aborted it as soon as Ankara made its objections clear.
The Turkish foreign ministry said Germany's Hamburg frigate stopped and searched the Roseline - a commercial vessel without permission on Sunday evening, off the coast of Greece's Peloponnesus peninsula.
Footage filmed by the vessel's crew and aired repeatedly on Turkish television showed a quarrel between crew members and armed German soldiers who landed on the ship from a helicopter.
The Turkish foreign ministry said the ship was carrying paint and humanitarian supplies headed to the Libyan port of Misrata.
"This intervention was carried out with the consent of neither our country as the flag state nor the ship's captain," the Turkish ministry said.
"I am strongly condemning this unlawful intervention," Turkish Vice President Fuat Oktay added.
But both the operation's European command and officials in Berlin said Turkey raised its objections only after the German soldiers had boarded the vessel.
"Everything went exactly according to protocol," a German foreign ministry spokeswoman said.
Operation Irini said in statement that it had "made good faith efforts to seek (Turkey's) consent".
"When (Turkey) made it clear that it denied the permission to inspect the vessel, Operation Irini suspended the activities during which no evidence of illicit material was found," it said.
Operation Irini's official website says the mission reserves the right to board ships without permission when conducting so-called "friendly approaches".
European warning
Libya has endured almost a decade of violence since the 2011 NATO-backed uprising that toppled and killed veteran dictator Moamer Kadhafi.
Turkey backs the UN-recognised Government of National Accord (GNA) in western Libya and views the EU mission as biased in favour of the eastern command - backed by the United Arab Emirates as well as Russia and France.
The warring sides agreed a ceasefire deal last month that paves the way for national elections on December 24.
But the process remains fragile and four EU powers involved in efforts to end the conflict issued a joint statement Monday threatening sanctions against "all Libyan and international parties" standing in the way of peace.
Operation Irini said the aborted inspection of the Turkish vessel was the fifth since the mission was officially launched on March 31.
Turkey last sparred with EU powers over inspections when a French frigate under NATO command sought in June to search a Tanzanian-flagged cargo ship.
Paris then complained that one of its ships was subjected to radar targeting by Turkish frigates while trying to inspect the cargo.
Ankara denied the charge.