Turkey on Monday said the German navy had conducted an "unauthorised" search on a Turkish-flagged vessel in a bid to enforce an arms embargo on Libya but only found humanitarian aid.

The European Union's Operation Irini, tasked with enforcing a United Nations arms embargo to Libya, has been headed by Turkey's regional rival Greece since last month.

The German frigate stopped and searched the commercial vessel without permission on Sunday evening off the coast of Greece's Peloponnesus peninsula, the Turkish foreign ministry said.

Operation Irini issued no immediate comment, but five EU powers involved in efforts to end the conflict in Libya -- including Germany -- issued a joint statement Monday threatening sanctions against "all Libyan and international parties" that harm the strife-torn country's peace process.

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 on a helicopter.

The soldiers stayed on board into the early hours of Monday, finding only biscuits and other humanitarian aid headed to the Libyan port of Misrata, Turkish media reports said.

The Turkish foreign ministry said it was protesting "this unauthorised action, which was carried out using force".

Turkey, which backs Libya's western UN-recognised Government of National Accord (GNA), views the EU mission as biased.

Ankara believes the EU ignores shipments sent to Libya's eastern strongman Khalifa Haftar -- especially by the United Arab Emirates -- who also enjoyed the backing of Russia, Egypt and France.

Libya has endured almost a decade of violence since the 2011 NATO-backed uprising that toppled and killed veteran dictator Moamer Kadhafi.

But there have been signs of progress, with last month's ceasefire formally ending fighting between Haftar's forces and the Tripoli-based GNA.

Operation Irini's official website says it reserves the right to board ships without permissions on so-called "friendly approaches".

In June, a French frigate under NATO command sought to inspect a Turkish cargo ship suspected of smuggling arms to Libya in violation of a UN embargo.

Paris then complained that one of its ships was subjected to radar targeting by Turkish frigates while trying to inspect the cargo.