Ukrainian authorities have arrested a Turkish-owned cargo ship and detained its captain over a visit it made to a port in Crimea after Russian annexed the peninsula from Ukraine last year.

Prosecutors said the Tuvalu-registered 5,095 deadweight tonne ship Kanton was being held in the Ukrainian port of Kherson. They said the crew could go to jail for up to three years and the ship could be seized.

The vessel's Istanbul-based owner, Master Shipping Ltd, called the detention illegal.

Russia seized Crimea shortly after Ukrainian protesters toppled a pro-Moscow president in February 2014. Ukraine has said any visit to Crimean ports is illegal, and a ban came into effect in July last year.

Master Shipping told Reuters on Friday that the Kanton called at Sevastopol in Crimea on July 24, 2014 to pick up a cargo of feed barley.

But it said this was before Ukraine had notified international shipping companies and insurers of the ban, and that Ukrainian authorities had later acknowledged this and cleared the vessel to enter other ports.

"The Ukrainian authorities have, despite their written permission, forcefully seized our papers and made the decision to detain our vessel after preventing the vessel's departure for 17 days," it said.

Master Shipping said the 12 crew members, mostly Turkish nationals, were on board the vessel, and none of them had been involved in the disputed Crimean visit.