Turkey said the vessel was carrying humanitarian aid and the soldiers had found nothing suspicious. German authorities also said they had not found anything suspicious by the time they were ordered off the ship.
“Everything went exactly according to protocol,” a German foreign ministry spokeswoman said.
Footage filmed by the vessel’s crew – and aired repeatedly on Turkish media – showed a quarrel between crew members and armed German soldiers who landed on the ship aboard 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 against “this unauthorised action, which was carried out using force”.
Turkish Foreign Ministry spokesman Hami Aksoy said: “The captain showed cooperation and shared information about the ship’s freight and its course. Despite this, at 17:45, armed forces from the Irini Operation boarded the ship and carried out a ‘monitoring’ that lasted long hours.
“We protest this act, which was carried out by force and without authorisation (and) retain the right to seek compensation,” he said.
The incident came amid rising tensions between Turkey and the EU. The bloc’s foreign policy chief has warned that ties are reaching a “watershed moment” over Turkish oil prospecting in waters claimed by Greece and Cyprus, saying that sanctions could be imposed next month.