The captain of the Oleg Naydenov said the ship was approached by a vessel flying the flag of Senegal, ITAR-Tass reported.
Vadim Mantorov said his ship was not using its trawl at the time but was in water open for fishing.
"Four military officers armed with automatic weapons embarked the ship from a high-speed boat lowered from the warship. In reply to my demands that they leave the ship and my statements that their actions were unlawful, I was told to follow them to Dakar. After my refusal, the military physically tried to force me, the captain, into their boat, but they were interrupted by the crew," Mantorov said.
Mantorov said some in his crew were injured, including a woman whose arm was broken. He said the Senegalese were especially rough on crew members from Guinea Bissau.
The Oleg Naydenov was being towed to Dakar.
Yuri Parshev, an executive with Feniks, the company that owns the ship, said the Oleg Naydenov operates in Guinea Bissau's 200-mile economic zone under an agreement that requires the ship employ and train some citizens of the African country. Parshev said the ship recently visited Dakar in Senegal to pick up a new Russian crew with no problems.
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