The EU on Monday froze the assets of Avrasya Shipping, whose cargo vessel Cirkin was involved in a naval incident between NATO members France and Turkey in June.
The EU has accused the company of using the ship to smuggle weapons to Libya. Ankara denies the arms-trafficking claim and says the ship was carrying humanitarian aid.
"The EU's Irini Operation is rewarding Haftar, and punishing the U.N.-recognised Libyan Government," Turkey's foreign ministry said on Wednesday, referring to the EU's military mission in the Mediterranean to stop arms from reaching warring factions in Libya.
Ankara has supported Libya's internationally recognised Government of National Accord based in Tripoli. Eastern Libya and much of the south, however, is controlled by Khalifa Haftar's Libyan National Army (LNA), which is backed by the United Arab Emirates (UAE), Egypt and Russia.
"Overlooking those countries and companies, starting with the UAE, that send weapons from land and air to the putschist Haftar in violation of the (United Nations Security Council) decisions, while the support provided to the legitimate government ... is deemed an embargo violation, is a clear signal that the EU is ... biased," Turkey's foreign ministry said.
In addition to sanctions on the Turkish company, the EU also imposed sanctions on two Libyan men, and two other companies - Kazakhstan's Sigma Airlines and Jordan's Med Wave Shipping.
Turkey may also face EU sanctions due to a dispute with Greece and Cyprus over ownership of natural resources in the eastern Mediterranean, although tensions between Ankara and Athens have declined in recent days.
"When effort is being made to decrease the tensions in the eastern Mediterranean, taking such a wrong decision is unfortunate," Turkey's foreign ministry said, referring to the sanctions on Avrasya Shipping.
(Reporting by Tuvan Gumrukcu and Ali Kucukgocmen; Editing by Tom Hogue)