Libya’s internationally recognized government says its forces attacked a Turkish-owned cargo vessel after it entered territorial waters off the North African country "without permission".

A senior member of the recognized parliament based in the eastern port city of Tobruk said late Monday that the ship was attacked after ignoring repeated warnings not to approach the port of Derna, a stronghold of militias and militants operating across the region.

"The air force called on it several times to turn back, but it failed to comply," media outlets quoted the lawmaker as saying.

The attack comes as the Tobruk-based government has frequently accused Turkish and Qatari governments of backing its rival militias based in the capital, Tripoli.

Meanwhile, Turkey’s Foreign Ministry has strongly condemned the deadly attack, saying that the ship was transporting a cargo to the Libyan port from Spain and came under attack when it was in international waters.

"We condemn strongly this contemptible attack which targeted a civilian ship in international waters and curse those who carried it out," the ministry said.

The ministry has also lodged a protest with Libyan authorities over the attack.

The ministry also noted that the third captain of the ship lost his life and several members of the crew sustained injuries in the attack, which happened early Monday when the MV Tuna 1, sailing under the flag of Cook Islands, tried to approach the shore.

Reports also said that the Turkish vessel caught fire and was towed in Tobruk terminal.

Libya plunged into chaos following the 2011 uprising against the dictatorship of Muammar Gaddafi, whose ouster gave rise to a patchwork of heavily-armed militia groups and deep political divisions.