"A vessel under the flag of Grenada, with a team of Turkish citizens on board, was detained," the east-based Libyan National Army Spokesman Ahmad al-Mismari was quoted by local media as saying.
The eastern forces stopped the ship in Libyan waters off the eastern city of Derna and questioned three crew members with Turkish passports, the spokesman said.
The ship was then dragged to a nearby port, Ras El Hilal, for "inspection and to verify its cargo," al-Mismari said.
It was not clear right now what the ship was carrying.
The news came amid growing cooperation between Ankara and Tripoli.
The UN-backed government of Libya on Thursday decided to activate two security memorandums of understanding (MoUs) signed with Turkey on November 27, Xinhua news agency reported.
One of the two MoUs is a maritime boundary deal that covers areas also claimed by Greece.
Turkey's Parliament on Saturday passed a security and military cooperation deal signed with the UN-backed Libyan government.
Turkish President Recep Tayyip Erdogan has said Turkey would have the right to deploy soldiers to Libya if it was invited by the UN-backed Libyan government.
General Khalifa Haftar, commander of the eastern-based army, declared recently the launch of the final stage of the military campaign in and around the Tripoli, ordering his troops to further advance into the city.
The east-based army and the UN-backed government have been fighting in and around Tripoli since early April over the control of the capital.
The conflicts killed and injured thousands of people, and displaced nearly 120,000 civil.
( With inputs from IANS )