Germany and the European Union are locked in a diplomatic spat with Turkey after an aborted vessel inspection in the Mediterranean Sea over the weekend.

German forces, part of EUNAVFOR MED's Operation Irini, stopped the 1,122-teu Turkey-flag containership Roseline A (built 1998) on Sunday, suspicious that it was violating the United Nations arms embargo on Libya.

Forces backed off after Turkish officials allegedly retroactively denied the inspection.

"We regret the detention of our ship, which seems to have not violated the arms embargo, from its route for hours under severe weather conditions, and the fact that the personnel were treated like criminals during the inspection," Turkish foreign ministry spokesman Hami Aksoy said in a statement on Monday, according to the English language Hurriyet Daily News.

"We protest this act of unauthorized and forceful use. All kinds of compensation rights of the relevant real and legal persons against the damages and losses that may arise from this will naturally be reserved."

According to an EU statement on Tuesday, Operation Irini officials requested the approval of Turkish flag state authorities four hours ahead of the boarding. They then gave an extra hour at the request of the Turkish embassy in Rome.

"Having received no answer from Turkey after the elapsed time, Operation Irini boarded the vessel and inspected it in accordance with internationally agreed procedures including Nato procedures," the EU statement said.

It said the forces left once Turkey informed them it did not consent to the boarding.

"Operation Irini's boarding team acted with the highest degree of professionalism and no incident was registered throughout the action," the EU said.

Germany's Ministry of Defence told the broadcaster DW that no contraband was found on board and the crew were cooperative.

EU forces scout a tanker. Photo: European Union

The Roseline A's registered owner is Arkas Konteyner Tasimacilik and it is managed by Arkas Denizcilik Ve Nakliyat. The manager shares an Istanbul address with Arkas Line, which lists the Roseline A on its online fleet list.

Arkas Line did not immediately return a request for comment.

Libya has been locked in a civil war since 2014, contested between the Government of National Accord (GNA) in the country's east and the Libyan National Army in the west.

Turkey reportedly supports the GNA, which is backed by the UN.

In late October, the two sides agreed to a UN-brokered ceasefire.

Operation Irini began in May. In September, TradeWinds reported it was stepping up inspections of vessels offshore Libya, as crude oil exports from the Opec member picked up.

That same month, the European Council sanctioned two companies, Med Wave Shipping and Avrasya Shipping, after they allegedly violated the arms embargo.

Med Wave has offices in Jordan and Lebanon, while Avrasya Shipping is based in Turkey.

The EU and Turkey are also in a dispute over Turkey's exploration for natural gas in waters claimed by EU members Greece and Cyprus. The EU has sanctioned Turkish individuals over this dispute.