The EU military mission, named Irini, is operating in the Mediterranean to stop arms from reach warring factions in Libya.
The mission said in a statement that a German frigate, supported by an Italian frigate, stopped the merchant vessel Royal Diamond 7 just after dawn in international waters, 150 km (95 miles) north of the Libyan city of Derna.
The ship had sailed from the port of Sharjah in the United Arab Emirates and was heading to Benghazi in Libya, the statement said, adding that its cargo of fuel was "likely to be used for military purposes".
The Royal Diamond 7 was diverted to an undisclosed EU port for further checks.
Libya has been split since 2014 between areas controlled by the internationally recognised Government of National Accord (GNA) in Tripoli and territory held by commander Khalifa Haftar's Libyan National Army (LNA), based in Benghazi.
The UAE, Egypt and Russia back Haftar, who has suffered a string of military reverses this year.
The U.N. Security Council has imposed an embargo on arms to stop the military confrontation and facilitate the peace process in the country.
The EU is enforcing the embargo through its Irini operation.
Turkish maritime news