A Russian-flagged ship carrying thousands of tonnes of wheat is being detained and investigated by Turkish authorities in the Black Sea port of Karasu over claims its cargo was stolen from Ukraine.

The action by Turkish customs officials comes after Kiev alleged that Zhibek Zholy was illegally transporting 7,000 tons of grain from Russian-occupied Berdyansk, a Ukrainian port in the country's southeast, the Telegraph reports.

Officials in Karasu said the vessel was waiting outside the port while investigations were undertaken into the origin of the shipment.

Russian Foreign Minister Sergei Lavrov confirmed the ship was Russian-flagged but appeared to muddy the waters as he claimed the Kremlin was seeking clarity on Monday.

"The ship is indeed Russian-flagged, but I think it belongs to Kazakhstan, and the cargo was being transported under a contract between Estonia and Turkey," Lavrov told reporters.

Kiev has accused Russia of stealing wheat from occupied Ukrainian territory to sell on international markets.

The country's wheat exports are responsible for almost 15 percent of the world total.

Zhibek Zholy's case has brought allegations of theft into focus and put the Turkish government in a vulnerable position as it continues to seek a mediating role between Moscow and Kiev on the global food supply issue.